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1

Mutations in the AGXT2L2 gene cause phosphohydroxylysinuria.  

PubMed

Phosphohydroxylysinuria has been described in two patients with neurological symptoms, but the deficient enzyme or mutated gene has never been identified. In the present work, we tested the hypothesis that this condition is due to mutations in the AGXT2L2 gene, recently shown to encode phosphohydroxylysine phospholyase. DNA analysis from a third patient, without neurological symptoms, but with an extreme hyperlaxicity of the joints, shows the existence of two mutations, p. Gly240Arg and p.Glu437Val, both in the heterozygous state. Sequencing of cDNA clones derived from fibroblasts mRNA indicated that the two mutations were allelic. Both mutations replace conserved residues. The mutated proteins were produced as recombinant proteins in Escherichia coli and HEK293T cells and shown to be very largely insoluble, whereas the wild-type one was produced as a soluble and active protein. We conclude that phosphohydroxylysinuria is due to mutations in the AGXT2L2 gene and the resulting lack of activity of phosphohydroxylysine phospholyase in vivo. The finding that the nul alleles of p.Gly240Arg and p.Glu437Val are present at low frequencies in the European and/or North American population suggests that this condition is more common than previously thought. The diversity of the clinical symptoms described in three patients with phosphohydroxylysinuria indicates that this is most likely not a neurometabolic disease. PMID:23242558

Veiga-da-Cunha, Maria; Verhoeven-Duif, Nanda M; de Koning, Tom J; Duran, Marinus; Dorland, Bert; Van Schaftingen, Emile

2012-12-14

2

In vivo evidence that Agxt2 can regulate plasma levels of dimethylarginines in mice.  

PubMed

Elevated plasma concentrations of the asymmetric (ADMA) and symmetric (SDMA) dimethylarginine have repeatedly been linked to adverse cardiovascular clinical outcomes. Both dimethylarginines can be degraded by alanine-glyoxylate aminotransferase 2 (Agxt2), which is also the key enzyme responsible for the degradation of endogenously formed ?-aminoisobutyrate (BAIB). In the present study we wanted to investigate the effect of BAIB on Agxt2 expression and Agxt2-mediated metabolism of dimethylarginines. We infused BAIB or saline intraperitoneally for 7days in C57/BL6 mice via minipumps. Expression of Agxt2 was determined in liver and kidney. The concentrations of BAIB, dimethylarginines and the Agxt2-specific ADMA metabolite ?-keto-?-(N(G),N(G)-dimethylguanidino)valeric acid (DMGV) was determined by LC-MS/MS in plasma and urine. As compared to controls systemic administration of BAIB increased plasma and urine BAIB levels by a factor of 26.5 (p<0.001) and 25.8 (p<0.01), respectively. BAIB infusion resulted in an increase of the plasma ADMA and SDMA concentrations of 27% and 31%, respectively, (both p<0.05) and a 24% decrease of plasma DMGV levels (p<0.05), while expression of Agxt2 was not different. Our data demonstrate that BAIB can inhibit Agxt2-mediated metabolism of dimethylarginines and show for the first time that endogenous Agxt2 is involved in the regulation of systemic ADMA, SDMA and DMGV levels. The effect of BAIB excess on endogenous dimethylarginine levels may have direct clinical implications for humans with the relatively common genetic trait of hyper-?-aminoisobutyric aciduria. PMID:23154179

Kittel, Anja; Maas, Renke; König, Jörg; Mieth, Maren; Weiss, Norbert; Jarzebska, Natalia; Hohenstein, Bernd; Martens-Lobenhoffer, Jens; Bode-Böger, Stefanie M; Rodionov, Roman N

2012-11-12

3

A double mutation in AGXT gene in families with primary hyperoxaluria type 1.  

PubMed

Primary hyperoxaluria type 1 (PH1) is a severe autosomal recessive inherited disorder of glyoxylate metabolism caused by mutations in the AGXT gene on chromosome 2q37.3 that encodes the hepatic peroxisomal enzyme alanine:glyoxylate aminotransferase. These mutations are found throughout the entire gene and cause a wide spectrum of clinical severity. Rare in Europe, PH1 is responsible for 13% of the end stage renal failure in the Tunisian child. In the present work, we identified the double mutation c.32C>T (Pro11Leu) and c.731T>C (p.Ile244Thr) in AGXT gene in five unrelated Tunisian families with PH1 disease. Our results provide evidence regarding the potential involvement of c.32C>T, originally described as common polymorphism, on the resulting phenotype. We also reported an extreme intrafamilial heterogeneity in clinical presentation of PH1. Despite the same genetic background, the outcome of the affected members differs widely. The significant phenotypic heterogeneity observed within a same family, with a same genotype, suggests the existence of relevant modifier factors. PMID:24012869

Kanoun, Houda; Jarraya, Faiçal; Hadj Salem, Ikhlass; Mahfoudh, Hichem; Chaabouni, Yosr; Makni, Fatma; Hachicha, Jamil; Fakhfakh, Faiza

2013-09-05

4

Probing AGXT2 enzyme activity in mouse tissue by applying stable isotope-labeled asymmetric dimethyl arginine as substrate.  

PubMed

Asymmetric dimethylarginine (ADMA) is a metabolite of the amino acid L-arginine. It competitively inhibits the enzymatic production of the cell-signaling substance nitric oxide. Therefore, increased levels of ADMA are associated with a range of cardiovascular and other diseases. ADMA is biologically eliminated by direct renal excretion and hydrolysis by the enzyme DDAH. Recently, a further elimination pathway via the transamination by the enzyme AGXT2 to ?-keto-?-(N(G),N(G)-dimethylguanidino)valeric acid (DMGV) has come into the focus of biological research. In this work, we describe an assay for the AGXT2 activity in mouse liver and kidney tissue. It is based on the transformation of isotope-labeled ADMA-d(6) to DMGV-d(6). The quantification of the DMGV-d(6) produced by this reaction in tissue homogenate samples was accomplished by chromatographic separation on a porous graphitic carbon column and tandem mass spectrometric detection. DMGV-d(6) with the deuterium labels in different molecular positions was used as internal standard. The overall production rates of DMGV-d(6) in mice were 195.37?pmol/min/mg total protein in liver and 85.21?pmol/min/mg total protein in kidney tissue, with coefficients of variation of 6.31% and 11.25%, respectively. This method can be applied as a tool for the characterization of the ADMA elimination by the AGXT2 pathway. PMID:23280748

Martens-Lobenhoffer, Jens; Rodionov, Roman N; Bode-Böger, Stefanie M

2012-12-01

5

MoGen, Inc  

Microsoft Academic Search

In 2006, Merrill Lynch became the lead book runner for a $5 billion convertible bond issue for MoGen, Inc., which was the single-largest convertible bond issuance in history. Merrill Lynch’s Equity Derivatives Group needed to convince MoGen’s management of the best coupon rate and conversion premium for MoGen and the potential investors in the issue. This pricing decision requires students

Kenneth Eades

6

GenBank  

Microsoft Academic Search

GenBank1 is a comprehensive database that con- tains publicly available DNA sequences for more than 165000 named organisms, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects. Most submissions are made using the web- based BankIt or standalone Sequin programs and accession numbers are assigned by GenBank staff upon receipt. Daily data exchange with the

Dennis A. Benson; Ilene Karsch-Mizrachi; David J. Lipman; James Ostell; David L. Wheeler

2003-01-01

7

GenBank  

Microsoft Academic Search

The GenBank ® sequence database incorporates publicly available DNA sequences of >55 000 different organisms, primarily through direct submission of sequence data from individual laboratories and large-scale sequencing projects. Most submissions are made using the BankIt (Web) or Sequin programs and accession numbers are assigned by GenBank staff upon receipt. Data exchange with the EMBL Data Library and the DNA

Dennis A. Benson; Ilene Karsch-Mizrachi; David J. Lipman; James Ostell; Barbara A. Rapp; David L. Wheeler

2000-01-01

8

GenBank.  

PubMed

GenBank® (http://www.ncbi.nlm.nih.gov) is a comprehensive database that contains publicly available nucleotide sequences for almost 260 000 formally described species. These sequences are obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole-genome shotgun (WGS) and environmental sampling projects. Most submissions are made using the web-based BankIt or standalone Sequin programs, and GenBank staff assigns accession numbers upon data receipt. Daily data exchange with the European Nucleotide Archive (ENA) and the DNA Data Bank of Japan (DDBJ) ensures worldwide coverage. GenBank is accessible through the NCBI Entrez retrieval system, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, begin at the NCBI home page: www.ncbi.nlm.nih.gov. PMID:23193287

Benson, Dennis A; Cavanaugh, Mark; Clark, Karen; Karsch-Mizrachi, Ilene; Lipman, David J; Ostell, James; Sayers, Eric W

2012-11-27

9

GenBank  

PubMed Central

GenBank® is a comprehensive database that contains publicly available DNA sequences for more than 165?000 named organisms, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects. Most submissions are made using the web-based BankIt or standalone Sequin programs and accession numbers are assigned by GenBank staff upon receipt. Daily data exchange with the EMBL Data Library in the UK and the DNA Data Bank of Japan helps to ensure worldwide coverage. GenBank is accessible through NCBI's retrieval system, Entrez, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, go to the NCBI Homepage at http://www.ncbi.nlm.nih.gov.

Benson, Dennis A.; Karsch-Mizrachi, Ilene; Lipman, David J.; Ostell, James; Wheeler, David L.

2005-01-01

10

GenBank  

PubMed Central

GenBank (R) is a comprehensive database that contains publicly available DNA sequences for more than 205?000 named organisms, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects. Most submissions are made using the Web-based BankIt or standalone Sequin programs and accession numbers are assigned by GenBank staff upon receipt. Daily data exchange with the EMBL Data Library in Europe and the DNA Data Bank of Japan ensures worldwide coverage. GenBank is accessible through NCBI's retrieval system, Entrez, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, go to the NCBI Homepage at .

Benson, Dennis A.; Karsch-Mizrachi, Ilene; Lipman, David J.; Ostell, James; Wheeler, David L.

2006-01-01

11

GenBank.  

PubMed

The GenBank((R))sequence database incorporates publicly available DNA sequences of >55 000 different organisms, primarily through direct submission of sequence data from individual laboratories and large-scale sequencing projects. Most submissions are made using the BankIt (Web) or Sequin programs and accession numbers are assigned by GenBank staff upon receipt. Data exchange with the EMBL Data Library and the DNA Data Bank of Japan helps ensure comprehensive worldwide coverage. GenBank data is accessible through NCBI's integrated retrieval system, Entrez, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping and protein structure information, plus the biomedical literature via PubMed. Sequence similarity searching is provided by the BLAST family of programs. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. NCBI also offers a wide range of WWW retrieval and analysis services based on GenBank data. The GenBank database and related resources are freely accessible via the NCBI home page at http://www.ncbi.nlm.nih.gov PMID:10592170

Benson, D A; Karsch-Mizrachi, I; Lipman, D J; Ostell, J; Rapp, B A; Wheeler, D L

2000-01-01

12

GenBank.  

PubMed

The GenBank nucleotide sequence database now contains sequence data and associated annotation corresponding to 85,000,000 nucleotides in 67,000 entries from a total of 3,000 organisms. The input stream of data coming into the database is primarily as direct submissions from the scientific community on electronic media, with little or no data being keyboarded from the printed page by the databank staff. The data are maintained in a relational database management system and are made available in flatfile form through on-line access, and through various network and off-line computer-readable media. The data are also distributed in relational form through satellite copies at a number of institutions in the U.S. and elsewhere. In addition, GenBank provides the U.S. distribution center for the BIOSCI electronic bulletin board service. PMID:1598235

Burks, C; Cinkosky, M J; Fischer, W M; Gilna, P; Hayden, J E; Keen, G M; Kelly, M; Kristofferson, D; Lawrence, J

1992-05-11

13

Taxonomic dissection of the genus Micrococcus: Kocuria gen. nov., Nesterenkonia gen. nov., Kytococcus gen. nov., Dermacoccus gen. nov., and Micrococcus Cohn 1872 gen. emend.  

PubMed

The results of a phylogenetic and chemotaxonomic analysis of the genus Micrococcus indicated that it is significantly heterogeneous. Except for Micrococcus lylae, no species groups phylogenetically with the type species of the genus, Micrococcus luteus. The other members of the genus form three separate phylogenetic lines which on the basis of chemotaxonomic properties can be assigned to four genera. These genera are the genus Kocuria gen. nov. for Micrococcus roseus, Micrococcus varians, and Micrococcus kristinae, described as Kocuria rosea comb. nov., Kocuria varians comb. nov., and Kocuria kristinae comb. nov., respectively; the genus Nesterenkonia gen. nov. for Micrococcus halobius, described as Nesterenkonia halobia comb. nov.; the genus Nesterenkonia gen. nov. for Micrococcus halobius, described as Nesterenkonia halobia comb. nov.; the genus Dermacoccus gen. nov. for Micrococcus nishinomiyaensis, described as Dermacoccus nishinomiyaensis comb. nov.; and the genus Kytocossus gen. nov. for Micrococcus sedentarius, described as Kytococcus sedentarius comb. nov. M. luteus and M. lylae, which are closely related phylogenetically but differ in some chemotaxonomic properties, are the only species that remain in the genus Micrococcus Cohn 1872. An emended description of the genus Micrococcus is given [corrected]. PMID:7547287

Stackebrandt, E; Koch, C; Gvozdiak, O; Schumann, P

1995-10-01

14

The GenBank genetic sequence databank.  

PubMed Central

The GenBank Genetic Sequence Data Bank contains over 5700 entries for DNA and RNA sequences that have been reported since 1967. This paper briefly describes the contents of the database, the forms in which the database is distributed, and the services we offer to scientists who use the GenBank database.

Bilofsky, H S; Burks, C; Fickett, J W; Goad, W B; Lewitter, F I; Rindone, W P; Swindell, C D; Tung, C S

1986-01-01

15

ReGen Collagen Scaffold (CS)  

Center for Biologics Evaluation and Research (CBER)

Text VersionPage 1. ReGen Collagen Scaffold (CS) Diana Zuckerman, Ph.D. President ... than nothing Page 17. Diana Zuckerman, Ph.D. President ... More results from www.fda.gov/downloads/advisorycommittees/committeesmeetingmaterials

16

77 FR 2342 - Fifth Meeting: RTCA, Next Gen Advisory Committee  

Federal Register 2010, 2011, 2012, 2013

...and Approve Recommendations for Submission to FAA Executive Level NextGen Implementation Metrics--an executive-level set of metrics that capture an overall status of NextGen implementation Other Business/Anticipated Issues for NAC...

2012-01-17

17

ReGen Biologics, Inc. Collagen Scaffold (CS)  

Center for Biologics Evaluation and Research (CBER)

Text Version... ReGen Biologics, Inc. Collagen Scaffold (CS) Page 2. 2 ... 12 Comparing the Use of Rotator Cuff Surgical Meshes with the ReGen Collagen Scaffold ... More results from www.fda.gov/downloads/advisorycommittees/committeesmeetingmaterials

18

VIEW OF GEN. LOGAN STATUE LOOKING SOUTHWEST WITH VISTA AS ...  

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

VIEW OF GEN. LOGAN STATUE LOOKING SOUTHWEST WITH VISTA AS TO THE GEN. THOMAS STATUE DOWN VERMONT AVENUE AND THE GEN. SCOTT STATUE DOWN RHODE ISLAND AVENUE IN THE BACKGROUND - Logan Circle, Vermont Avenue, Rhode Island Avenue, & Thirteenth Street, Washington, District of Columbia, DC

19

PlayGen: A HYBRID PLAYLIST GENERATOR  

Microsoft Academic Search

Although automatic playlist generation (APG) has gained interest lately due to the recent popularity of Electronic Music Distribution (EMD) systems, it is still in research and development state. Researchers have come up with similarity based techniques and constrained based techniques to generate playlists automatically. This paper, for the first time, presents an APG technique, PlayGen, which is a hybrid of

Indika Kahanda; K. S Walgama; R. G Ragel

20

Quina és la funció del gen clonat?  

Microsoft Academic Search

Presentem una activitat didàctica complementària per a alumnes de segon de batxillerat. A partir d’una seqüència de nucleòtids del genoma de Paenibacillus barcinonensis determinem la regió codificant d’un gen, la proteïna corresponent i la seva funció. Com a annex s’inclou el guió per a l’alumnat.

Margarita Soriano; Francisca Guerola

2008-01-01

21

The Integrated Airport: Building a Successful NextGen Testbed  

SciTech Connect

This presentation will describe a unique public-private partnership - the Integrated Airport - that was created to engage in research and testing related to NextGen Technology deployment. NextGen refers to the program that will be initiated to modernize the US National Airspace. As with any major, multi-decade initiative, such as NextGen, integration of work efforts by multiple partners in the modernization is critical for success. This talk will focus on the development of the consortium, how the consortium plans for NextGen initiatives, the series of technology demonstrations we have produced and plans for the future of NextGen testing and implementation.

Frederick-Recascino, Christina (Embry-Riddle Aeronautical University); Sweigard, Doug (Lockheed Martin Corporation); Lester, Wade (ERAU)

2009-02-18

22

The Integrated Airport: Building a Successful NextGen Testbed  

ScienceCinema

This presentation will describe a unique public-private partnership - the Integrated Airport - that was created to engage in research and testing related to NextGen Technology deployment. NextGen refers to the program that will be initiated to modernize the US National Airspace. As with any major, multi-decade initiative, such as NextGen, integration of work efforts by multiple partners in the modernization is critical for success. This talk will focus on the development of the consortium, how the consortium plans for NextGen initiatives, the series of technology demonstrations we have produced and plans for the future of NextGen testing and implementation.

23

Gen IV Materials Handbook Implementation Plan  

SciTech Connect

A Gen IV Materials Handbook is being developed to provide an authoritative single source of highly qualified structural materials information and materials properties data for use in design and analyses of all Generation IV Reactor Systems. The Handbook will be responsive to the needs expressed by all of the principal government, national laboratory, and private company stakeholders of Gen IV Reactor Systems. The Gen IV Materials Handbook Implementation Plan provided here addresses the purpose, rationale, attributes, and benefits of the Handbook and will detail its content, format, quality assurance, applicability, and access. Structural materials, both metallic and ceramic, for all Gen IV reactor types currently supported by the Department of Energy (DOE) will be included in the Gen IV Materials Handbook. However, initial emphasis will be on materials for the Very High Temperature Reactor (VHTR). Descriptive information (e.g., chemical composition and applicable technical specifications and codes) will be provided for each material along with an extensive presentation of mechanical and physical property data including consideration of temperature, irradiation, environment, etc. effects on properties. Access to the Gen IV Materials Handbook will be internet-based with appropriate levels of control. Information and data in the Handbook will be configured to allow search by material classes, specific materials, specific information or property class, specific property, data parameters, and individual data points identified with materials parameters, test conditions, and data source. Details on all of these as well as proposed applicability and consideration of data quality classes are provided in the Implementation Plan. Website development for the Handbook is divided into six phases including (1) detailed product analysis and specification, (2) simulation and design, (3) implementation and testing, (4) product release, (5) project/product evaluation, and (6) product maintenance and enhancement. Contracting of development of the Handbook website is discussed in terms of host server options, cost, technology, developer background and cooperative nature, and company stability. One of the first and most important activities in website development will be the generation of a detailed Handbook product requirements document including case diagrams and functional requirements tables. The Implementation Plan provides a detailed overview of the organizational structure of the Handbook and details of Handbook preparation, publication, and distribution. Finally, the Implementation Plan defines Quality Assurance requirements for the Handbook.

Rittenhouse, P.; Ren, W.

2005-03-29

24

Complications Following BellaGen(TM) Injection  

PubMed Central

BellaGen™ is an injectable acellular dermal matrix granule derived from donated human skin tissue that was recently developed for soft tissue augmentation. Its use has been sporadically reported in penile girth enhancement procedures. Many cases of complications have been reported after injecting acellular dermal matrices like AlloDerm or SureDerm™ but few reports on complications associated with BellaGen™ injection. We report here on penile skin inflammation and necrosis following augmentation phalloplasty with BellaGen™, which developed 3 days after the injection and persisted for more than 2 weeks. The patient had a 15 year history of type 2 diabetes mellitus, and he was treated with oral antibiotics and wet dressings with KMNO4 solution to combine preservation of the remaining penile soft tissue with debridement of avascular tissue. The lesion improved with this treatment, but the patient experienced pain for about 2 weeks. All patients should be informed of the potential complications with the use of injectable acellular dermal matrices before treatment. Patient selection for augmentation is also important to have the most desirable results.

Park, Mi Kyung; Kim, Hyun Kyu; Park, Kui Young; Li, Kapsok; Hong, Chang Kwun

2011-01-01

25

Gen IV Materials Handbook Functionalities and Operation  

SciTech Connect

This document is prepared for navigation and operation of the Gen IV Materials Handbook, with architecture description and new user access initiation instructions. Development rationale and history of the Handbook is summarized. The major development aspects, architecture, and design principles of the Handbook are briefly introduced to provide an overview of its past evolution and future prospects. Detailed instructions are given with examples for navigating the constructed Handbook components and using the main functionalities. Procedures are provided in a step-by-step fashion for Data Upload Managers to upload reports and data files, as well as for new users to initiate Handbook access.

Ren, Weiju [ORNL

2009-12-01

26

Towards an International Culture: Gen Y Students and SNS?  

ERIC Educational Resources Information Center

|This article reports the findings of a small-scale investigation into the Internet user behaviour of generation Y (Gen Y) students, with particular reference to social networking sites. The study adds to the literature on cross-cultural Internet user behaviour with specific reference to Gen Y and social networking. It compares how a cohort of…

Lichy, Jessica

2012-01-01

27

Palerasnitsynus gen. n. (Trichoptera, Psychomyiidae) from Burmese amber  

PubMed Central

Abstract Palerasnitsynus ohlhoffi gen. et sp. n. is described fromBurmese amber of late Albian (Lower Cretaceous) age. This is the first record of the family Psychomyiidae from Burmese amber, and the earliest fossil record of the family. The genus Palerasnitsynus gen. n. differs from all other known psychomyiid genera by the absence of fork III in the forewings.

Wichard, Wilfried; Ross, Emma; Ross, Andrew J.

2011-01-01

28

The integrated airport — A NextGen test bed  

Microsoft Academic Search

The Next Generation Air Transportation System (NextGen) will significantly increase the safety, security, and capacity of air transportation operations in order to handle the dramatic increases in air traffic that are forecast by 2025 New technology, procedures, and airport infrastructure will be required in order to evolve Federal Aviation Administration (FAA) and aviation industry systems to meet these challenges. NextGen

M. W. Burkle; T. E. Montgomery

2008-01-01

29

Head-worn displays for NextGen  

NASA Astrophysics Data System (ADS)

The operating concepts emerging under the Next Generation air transportation system (NextGen) require new technology and procedures - not only on the ground-side - but also on the flight deck. Flight deck display and decision support technologies are specifically targeted to overcome aircraft safety barriers that might otherwise constrain the full realization of NextGen. One such technology is the very lightweight, unobtrusive head-worn display (HWD). HWDs with an integrated head-tracking system are being researched as they offer significant potential benefit under emerging NextGen operational concepts. Two areas of benefit for NextGen are defined. First, the HWD may be designed to be equivalent to the Head-Up Display (HUD) using Virtual HUD concepts. As such, these operational credits may be provided to significantly more aircraft for which HUD installation is neither practical nor possible. Second, the HWD provides unique display capabilities, such as an unlimited field-of-regard. These capabilities may be integral to emerging NextGen operational concepts, eliminating safety issues which might otherwise constrain the full realization of NextGen. The paper details recent research results, current HWD technology limitations, and future technology development needed to realize HWDs as a enabling technology for NextGen.

Bailey, Randall E.; Shelton, Kevin J.; Arthur, J. J., III

2011-05-01

30

GenR, an IclR-Type Regulator, Activates and Represses the Transcription of gen Genes Involved in 3-Hydroxybenzoate and Gentisate Catabolism in Corynebacterium glutamicum  

PubMed Central

The genes required for 3-hydroxybenzoate and gentisate catabolism in Corynebacterium glutamicum are closely clustered in three operons. GenR, an IclR-type regulator, can activate the transcription of genKH and genDFM operons in response to 3-hydroxybenzoate and gentisate, and it can repress its own expression. Footprinting analyses demonstrated that GenR bound to four sites with different affinities. Two GenR-binding sites (DFMn01 and DFMn02) were found to be located between positions ?41 and ?84 upstream of the ?35 and ?10 regions of the genDFM promoter, which was involved in positive regulation of genDFM transcription. The GenR binding site R-KHn01 (located between positions ?47 and ?16) overlapped the ?35 region of the genKH promoter sequence and is involved in positive regulation of its transcription. The binding site R-KHn02, at which GenR binds to its own promoter, was found within a footprint extending from position ?44 to ?67. It appeared to be involved in negative regulation of the activity of the genR promoter. A consensus motif with a 5-bp imperfect palindromic sequence [ATTCC-N7(5)-GGAAT] was identified among all four GenR binding sites and found to be necessary to GenR regulation through site-directed mutagenesis. The results reveal a new regulatory function of the IclR family in the catabolism of aromatic compounds.

Chao, Hongjun

2013-01-01

31

98. SWITCH HOUSE MAIN LOBBY, GEN 3 CIRCUIT BREAKER, VIEW ...  

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

98. SWITCH HOUSE MAIN LOBBY, GEN 3 CIRCUIT BREAKER, VIEW OF OPPOSITE SIDE FROM HAER No. PA-505-97 - Delaware County Electric Company, Chester Station, Delaware River at South end of Ward Street, Chester, Delaware County, PA

32

GEN #6 ** treatment A: test ; ** treatment B: reference ...  

Center for Drug Evaluation (CDER)

GEN #6 ** treatment A: test ; ** treatment B: reference ; ** variables : Subj sex age weight sequence period trt CMAX AUCI AUCT; *Subj SEX AGE ... More results from www.fda.gov/downloads/drugs/scienceresearch

33

Sources of data in the GenBank database  

SciTech Connect

The citations in GenBank are characterized with respect to form of publication. The potential spectrum of quality control problems applicable to the various types of unpublished data are discussed. 6 refs., 2 tabs.

Burks, C.

1987-01-01

34

A Novel Role of Human Holliday Junction Resolvase GEN1 in the Maintenance of Centrosome Integrity  

PubMed Central

The maintenance of genomic stability requires accurate genome replication, repair of DNA damage, and the precise segregation of chromosomes in mitosis. GEN1 possesses Holliday junction resolvase activity in vitro and presumably functions in homology driven repair of DNA double strand breaks. However, little is currently known about the cellular functions of human GEN1. In the present study we demonstrate that GEN1 is a novel centrosome associated protein and we characterize the various phenotypes associated with GEN1 deficiency. We identify an N-terminal centrosome localization signal in GEN1, which is required and sufficient for centrosome localization. We report that GEN1 depletion results in aberrant centrosome numbers associated with the formation of multiple spindle poles in mitosis, an increased number of cells with multi-nuclei, increased apoptosis and an elevated level of spontaneous DNA damage. We find homologous recombination severely impaired in GEN1 deficient cells, suggesting that GEN1 functions as a Holliday junction resolvase in vivo as well as in vitro. Complementation of GEN1 depleted cells with various GEN1 constructs revealed that centrosome association but not catalytic activity of GEN1 is required for preventing centrosome hyper-amplification, formation of multiple mitotic spindles, and multi-nucleation. Our findings provide novel insight into the biological functions of GEN1 by uncovering an important role of GEN1 in the regulation of centrosome integrity.

Zhou, Dong-Ping; Xu, Qian; Li, Miao-Miao; Wang, Zhao-Qi; Tong, Wei-Min; Yang, Yun-Gui

2012-01-01

35

Genes and proteins of Escherichia coli (GenProtEc).  

PubMed

GenProtEc is a database of Escherichia coli genes and their gene products, classified by type of function and physiological role and with citations to the literature for each. Also present are data on sequence similarities among E.coli proteins with PAM values, percent identity of amino acids, length of alignment and percent aligned. The database is available as a PKZip file by ftp from mbl.edu/pub/ecoli.exe. The program runs under MS-DOS on IMB-compatible machines. GenProtEc can also be accessed through the World Wide Web at URL http://mbl.edu/html/ecoli.html. PMID:8594596

Riley, M; Space, D B

1996-01-01

36

A Virtual Reality Framework to Optimize Design, Operation and Refueling of GEN-IV Reactors.  

SciTech Connect

many GEN-IV candidate designs are currently under investigation. Technical issues related to material, safety and economics are being addressed at research laboratories, industry and in academia. After safety, economic feasibility is likely to be the most important crterion in the success of GEN-IV design(s). Lessons learned from the designers and operators of GEN-II (and GEN-III) reactors must play a vital role in achieving both safety and economic feasibility goals.

Rizwan-uddin; Nick Karancevic; Stefano Markidis; Joel Dixon; Cheng Luo; Jared Reynolds

2008-04-23

37

GEN-SYSTEM - A new experimental philosophy for EISCAT radars  

Microsoft Academic Search

GEN-SYSTEM is a code name for a new experimental design philosphy, a set of related correlator algorithms and an experiment library based on this philosophy. It is designed to obtain an easy way to develop powerful experiments having several different modulations in the same pattern or to have very powerful modulations in single channel experiments, needed sometimes in special applications.

Tauno Turunen

1986-01-01

38

A New Parent Generation: Meet Mr. and Mrs. Gen X  

ERIC Educational Resources Information Center

|Slowly but surely, Generation Xers have been taking over from Baby Boomers as the majority of parents in elementary and secondary education. Gen-X parents and Boomer parents belong to two neighboring generations, each possessing its own location in history and its own peer personality. They are similar in some respects, but clearly different in…

Howe, Neil

2010-01-01

39

An electronic flight bag for NextGen avionics  

NASA Astrophysics Data System (ADS)

The introduction of the Next Generation Air Transportation System (NextGen) initiative by the Federal Aviation Administration (FAA) will impose new requirements for cockpit avionics. A similar program is also taking place in Europe by the European Organisation for the Safety of Air Navigation (Eurocontrol) called the Single European Sky Air Traffic Management Research (SESAR) initiative. NextGen will require aircraft to utilize Automatic Dependent Surveillance-Broadcast (ADS-B) in/out technology, requiring substantial changes to existing cockpit display systems. There are two ways that aircraft operators can upgrade their aircraft in order to utilize ADS-B technology. The first is to replace existing primary flight displays with new displays that are ADS-B compatible. The second, less costly approach is to install an advanced Class 3 Electronic Flight Bag (EFB) system. The installation of Class 3 EFBs in the cockpit will allow aircraft operators to utilize ADS-B technology in a lesser amount of time with a decreased cost of implementation and will provide additional benefits to the operator. This paper describes a Class 3 EFB, the NexisTM Flight-Intelligence System, which has been designed to allow users a direct interface with NextGen avionics sensors while additionally providing the pilot with all the necessary information to meet NextGen requirements.

Zelazo, D. Eyton

2012-05-01

40

Boomers, Gen-Xers, and Millennials: Understanding the "New Students."  

ERIC Educational Resources Information Center

Describes characteristics of the "new" college student, who may be an adult learner from the Baby Boomer era, a high school member of the "Millennial" generation, or a "Gen-Xer." Explores the learning styles of each type of student and discusses the importance of technology to each group. (SLD)

Oblinger, Diana

2003-01-01

41

Meet Mr. and Mrs. Gen X: A New Parent Generation  

ERIC Educational Resources Information Center

Slowly but surely, Generation Xers have been taking over from Baby Boomers as the majority of parents in elementary and secondary education. In the early 1990s, Gen Xers began joining parent-teacher associations in the nation's elementary schools. Around 2005, they became the majority of middle school parents. By the fall of 2008, they took over…

Howe, Neil

2010-01-01

42

AdGVVEGF121.10 (GenVec).  

PubMed

GenVec, in collaboration with Pfizer (formerly Parke-Davis), is developing AdGVVEGF121.10 (BioBypass), a gene therapy involving the 121-residue isoform of vascular endothelial growth factor (VEGF), licensed from Scios, for the potential treatment of coronary artery disease (CAD) and peripheral vascular disease (PVD) [262000]. By March 2000, phase II trials in CAD had commenced [359531], [359532], [359538]. By August 2000, phase II trials were also underway for PVD [386293]. The initial phase II trial will include approximately 70 patients with severe CAD who are not candidates for bypass surgery and will assess exercise capacity and patient well-being, before and after treatment, as well as safety and drug tolerance [364137]. Scios licensed the gene transfer applications of VEGF121 to GenVec in June 1996 [263381]. In September 1997, GenVec entered into an agreement with Parke-Davis, a subsidiary of Warner-Lambert (now Pfizer), to develop the therapy [262000]. In May 1999, Warner-Lambert signed an agreement with Bioscience for a device for the administration of AdGVVEGF121.10 1325443]. In May 2000, Merrill Lynch predicted a US filing in the first half of 2003 [375962]. In January 2001, AG Edwards predicted the product would generate $70 million in revenues to Pfizer and $12 million in royalties to GenVec in 2005. In February 1999, GenVec was awarded US-05846782, covering vectors for targeting the transfer of therapeutic genes to specific tissues in the human body [316038]. PMID:11572658

Basara, N

2001-06-01

43

A New Genus of Actinomycetales--Promicromonospora gen. nov. (Novyu Rod Luchistikh Gribkov--Promicromonospora gen. nov.).  

National Technical Information Service (NTIS)

The organism Promicromonospora citrea n. gen. n. sp has been described. The culture grows well on many synthetic and organic media. The colonies on many media (MPA, Medium 1 with starch, starch-ammonia agar, potato agar) are of yellowish color, naked or c...

N. A. Krasilnikov L. V. Kalakutskii N. F. Kirillova

1971-01-01

44

DOE/NNSA perspective safeguard by design: GEN III/III+ light water reactors and beyond  

SciTech Connect

An overview of key issues relevant to safeguards by design (SBD) for GEN III/IV nuclear reactors is provided. Lessons learned from construction of typical GEN III+ water reactors with respect to SBD are highlighted. Details of SBD for safeguards guidance development for GEN III/III+ light water reactors are developed and reported. This paper also identifies technical challenges to extend SBD including proliferation resistance methodologies to other GEN III/III+ reactors (except HWRs) and GEN IV reactors because of their immaturity in designs.

Pan, Paul Y [Los Alamos National Laboratory

2010-12-10

45

GenNet: A Platform for Hybrid Network Experiments  

PubMed Central

We describe General Network (GenNet), a software plugin for the real time experimental interface (RTXI) dynamic clamp system that allows for straightforward and flexible implementation of hybrid network experiments. This extension to RTXI allows for hybrid networks that contain an arbitrary number of simulated and real neurons, significantly improving upon previous solutions that were limited, particularly by the number of cells supported. The benefits of this system include the ability to rapidly and easily set up and perform scalable experiments with hybrid networks and the ability to scan through ranges of parameters. We present instructions for installing, running and using GenNet for hybrid network experiments and provide several example uses of the system.

Kispersky, Tilman J.; Economo, Michael N.; Randeria, Pratik; White, John A.

2011-01-01

46

GenPhyloData: realistic simulation of gene family evolution  

PubMed Central

Background PrIME-GenPhyloData is a suite of tools for creating realistic simulated phylogenetic trees, in particular for families of homologous genes. It supports generation of trees based on a birth-death process and—perhaps more interestingly—also supports generation of gene family trees guided by a known (synthetic or biological) species tree while accounting for events such as gene duplication, gene loss, and lateral gene transfer (LGT). The suite also supports a wide range of branch rate models enabling relaxation of the molecular clock. Result Simulated data created with PrIME-GenPhyloData can be used for benchmarking phylogenetic approaches, or for characterizing models or model parameters with respect to biological data. Conclusion The concept of tree-in-tree evolution can also be used to model, for instance, biogeography or host-parasite co-evolution.

2013-01-01

47

Critical Issues on Materials for Gen-IV Reactors  

Microsoft Academic Search

Within the LDRD on 'Critical Issues on Materials for Gen-IV Reactors' basic thermodynamics of the Fe-Cr alloy and accurate atomistic modeling were used to help develop the capability to predict hardening, swelling and embrittlement using the paradigm of Multiscale Materials Modeling. Approaches at atomistic and mesoscale levels were linked to build-up the first steps in an integrated modeling platform that

M Caro; J Marian; E Martinez; P Erhart

2009-01-01

48

Technology evaluation: C242-DM1, ImmunoGen Inc.  

PubMed

C242-DM1 is a tumor-activated immunotoxin under development by GlaxoSmithKline plc (formerly SmithKline Beecham plc), under licence from ImmunoGen Inc, as a potential treatment for colon tumor. It consists of a colon cancer-specific humanized antibody, C242, conjugated to the maytansine derivative DM1. In preclinical studies, C242-DM1 caused complete tumor regression in animal models of both human pancreatic and non-small cell lung cancer (NSCLC) at non-toxic doses. C242-DM1 has also been evaluated in an immunoconjugate combination with J-591 (Cornell University). The J591-DM1 immunoconjugate demonstrated effective, antigen-specific delivery of a highly cytotoxic drug to PSMA-positive Pca cells in vitro and in vivo with low systemic toxicity. Results from studies in monkeys showed that C242-DM1 had no significant toxicity or side effects, when administered at doses higher than those that were previously shown to completely eradicate human colon tumors in mice [271420]. ImmunoGen acquired the right to evaluate, and an option to license, technology related to maytansines from Takeda. In February 1999, ImmunoGen and SmithKline Beecham signed a US $45 million development and commercialization agreement for C242-DM1 [313493]. In August 1997, Immunogen received an SBIR grant to advance development of huC242-DM1 [258356]. EP-00425235, held by ImmunoGen, covers conjugated forms of ansamitocin (maytansine) derivatives. Takeda holds several patents for the production of ansamitocin and its analogs, the first one being JP-53124692. PMID:11338934

Smith, S

2001-04-01

49

Coal-Gen attendees hear there's no magic bullet  

SciTech Connect

Those attending COAL-GEN 2007 in August heard that there is no magic bullet for meeting the energy and infrastructure needs facing the USA. The article reports on the conference which addressed topics including development of supercritical circulating fluidized bed coal unit; IGCC projects, the importance of including carbon capture and sequestration, and the need to attract and train personnel to work in the power industry. 3 photos.

NONE

2007-09-15

50

J3Gen: a PRNG for low-cost passive RFID.  

PubMed

Pseudorandom number generation (PRNG) is the main security tool in low-cost passive radio-frequency identification (RFID) technologies, such as EPC Gen2. We present a lightweight PRNG design for low-cost passive RFID tags, named J3Gen. J3Gen is based on a linear feedback shift register (LFSR) configured with multiple feedback polynomials. The polynomials are alternated during the generation of sequences via a physical source of randomness. J3Gen successfully handles the inherent linearity of LFSR based PRNGs and satisfies the statistical requirements imposed by the EPC Gen2 standard. A hardware implementation of J3Gen is presented and evaluated with regard to different design parameters, defining the key-equivalence security and nonlinearity of the design. The results of a SPICE simulation confirm the power-consumption suitability of the proposal. PMID:23519344

Melià-Seguí, Joan; Garcia-Alfaro, Joaquin; Herrera-Joancomartí, Jordi

2013-03-19

51

J3Gen: A PRNG for Low-Cost Passive RFID  

PubMed Central

Pseudorandom number generation (PRNG) is the main security tool in low-cost passive radio-frequency identification (RFID) technologies, such as EPC Gen2. We present a lightweight PRNG design for low-cost passive RFID tags, named J3Gen. J3Gen is based on a linear feedback shift register (LFSR) configured with multiple feedback polynomials. The polynomials are alternated during the generation of sequences via a physical source of randomness. J3Gen successfully handles the inherent linearity of LFSR based PRNGs and satisfies the statistical requirements imposed by the EPC Gen2 standard. A hardware implementation of J3Gen is presented and evaluated with regard to different design parameters, defining the key-equivalence security and nonlinearity of the design. The results of a SPICE simulation confirm the power-consumption suitability of the proposal.

Melia-Segui, Joan; Garcia-Alfaro, Joaquin; Herrera-Joancomarti, Jordi

2013-01-01

52

A direct drive permanent magnet generator design for a tidal current turbine(SeaGen)  

Microsoft Academic Search

In this study, the feasibility of a direct-drive per- manent magnet generator for a tidal turbine power take-off system, namely MCT's SeaGen -the world's first full scale commercial tidal turbine- has been investigated. The investigated PM generator topology is called C-GEN which is an air-cored axial-flux generator developed in the University of Edinburgh. The C-GEN is prior to conventional PM

Ozan Keysan; Alasdair S. McDonald; Markus Mueller

2011-01-01

53

ZeroGen new generation power–a framework for engaging stakeholders  

Microsoft Academic Search

ZeroGen Pty Ltd (ZeroGen) recently announced its plan to develop the world’s first commercial-scale 450MW clean coal power plant by 2017 in Queensland, Australia. Since the Queensland Government first announced the project in early 2006, stakeholder engagement activities have been a key priority for ZeroGen. The company understands that stakeholder perceptions, particularly of the safety of carbon dioxide (CO2) capture

Peta Simpson; Peta Ashworth

2009-01-01

54

Endosporoideus gen. nov., a mitosporic fungus on Phoenix hanceana.  

PubMed

Endosporoideus pedicellata gen. et sp, nov. is described and illustrated from decaying petioles of Phoenix hanceana collected from grassland in Tai Mo Shan, Hong Kong. The genus is unique in producing solitary, phragmosporous conidia. The conidia comprise a brown to dark brown inner-wall layer and thick, hyaline outer-wall layer and are produced holoblastically from determinate conidiogenous cells on micronematous, mononematous conidiophores. Cells of conidia may disarticulate at the septa. Representative steps in conidiogenesis of E. pedicellata are illustrated with light micrographs, and details of the conidiogenous events are interpreted schematically. PMID:16389975

Ho, Wai Hong; Yanna; Hyde, Kevin D; Goh, Teik Khiang

55

Meloneis Gen. Nov., a New Epipsammic Genus of Rhaphoneidaceae (Bacillariophyceae)  

PubMed Central

The diatom family Rhaphoneidaceae is characterized by high generic diversity and low species diversity with most genera known to have long stratigraphic ranges. The genera within this family are neritic marine, and mostly epipsammic. A new modern and epipsammic genus, Meloneis gen. nov., is described herein and is compared to all genera within Rhaphoneidaceae and especially to Rhaphoneis Ehrenberg s.l. Within Meloneis three new species and one variety are distinguished and described herein: M. mimallis sp. nov., M. mimallis var. zephyria var. nov., M. akytos sp. nov., and M. gorgis sp. nov.

Louvrou, Ioanna; Danielidis, Daniel B.; Economou-Amilli, Athena

2012-01-01

56

Influence of tidal parameters on SeaGen flicker performance.  

PubMed

This paper presents the analysis of the study of the flicker emitted from the 1.2?MW tidal energy converter (TEC), SeaGen, against varying tidal parameters. This paper outlines the main elements of the TEC itself, the environment it is located in and the measurement set up. In this paper, the flicker emitted by the TEC is compared with the different tidal parameters, including flood and ebb tides, tidal speed, water depth and turbulence strength and intensity. Flicker emissions have been calculated from measured data in over 90 measurement (10?min) periods, and all of the tidal parameters vary significantly over that testing period. This allows for a detailed statistical and graphical analysis of the variation of flicker with the variation of the tidal parameters outlined above. It is found, with the exception of tidal speed, that there is no strong relationship between flicker emissions and any other tidal parameter. As SeaGen is an asymmetrical TEC with full blade pitching for flood and ebb generation, it was also found that the expected difference of flicker emissions owing to the effect of the submersed crossbeam was not significant. The TEC harmonic performance versus tidal speed is also presented. PMID:23319709

MacEnri, Joseph; Reed, Matthew; Thiringer, Torbjörn

2013-01-14

57

GenGIS: A geospatial information system for genomic data  

PubMed Central

The increasing availability of genetic sequence data associated with explicit geographic and ecological information is offering new opportunities to study the processes that shape biodiversity. The generation and testing of hypotheses using these data sets requires effective tools for mathematical and visual analysis that can integrate digital maps, ecological data, and large genetic, genomic, or metagenomic data sets. GenGIS is a free and open-source software package that supports the integration of digital map data with genetic sequences and environmental information from multiple sample sites. Essential bioinformatic and statistical tools are integrated into the software, allowing the user a wide range of analysis options for their sequence data. Data visualizations are combined with the cartographic display to yield a clear view of the relationship between geography and genomic diversity, with a particular focus on the hierarchical clustering of sites based on their similarity or phylogenetic proximity. Here we outline the features of GenGIS and demonstrate its application to georeferenced microbial metagenomic, HIV-1, and human mitochondrial DNA data sets.

Parks, Donovan H.; Porter, Michael; Churcher, Sylvia; Wang, Suwen; Blouin, Christian; Whalley, Jacqueline; Brooks, Stephen; Beiko, Robert G.

2009-01-01

58

Next gen wavelets down-sampling preserving statistics  

NASA Astrophysics Data System (ADS)

We extend the 2nd Gen Discrete Wavelet Transform (DWT) of Swelden to the Next Generations (NG) Digital Wavelet Transform (DWT) preserving the statistical salient features. The lossless NG DWT accomplishes the data compression of "wellness baseline profiles (WBP)" of aging population at homes. For medical monitoring system at home fronts we translate the military experience to dual usage of veterans & civilian alike with the following three requirements: (i) Data Compression: The necessary down sampling reduces the immense amount of data of individual WBP from hours to days and to weeks for primary caretakers in terms of moments, e.g. mean value, variance, etc., without the artifacts caused by FFT arbitrary windowing. (ii) Lossless: our new NG_DWT must preserve the original data sets. (iii) Phase Transition: NG_DWT must capture the critical phase transition of the wellness toward the sickness with simultaneous display of local statistical moments. According to the Nyquist sampling theory, assuming a band-limited wellness physiology, we must sample the WBP at least twice per day since it is changing diurnally and seasonally. Since NG_DWT, like the 2nd Gen, is lossless, we can reconstruct the original time series for the physicians' second looks. This technique of NG_DWT can also help stock market day-traders monitoring the volatility of multiple portfolios without artificial horizon artifacts.

Szu, Harold; Miao, Lidan; Chanyagon, Pornchai; Cader, Masud

2007-04-01

59

77 FR 25524 - Sixth Meeting: RTCA, NextGen Advisory Committee  

Federal Register 2010, 2011, 2012, 2013

...and Approve Recommendation for Submission to FAA NextGen Implementation Metrics--a recommendation for an executive-level set of metrics that capture an overall status of NextGen implementation 10:45-11:15 Break 11:15-12:15...

2012-04-30

60

GenBank and PubMed: How connected are they?  

PubMed Central

Background GenBank(R) is a public repository of all publicly available molecular sequence data from a range of sources. In addition to relevant metadata (e.g., sequence description, source organism and taxonomy), publication information is recorded in the GenBank data file. The identification of literature associated with a given molecular sequence may be an essential first step in developing research hypotheses. Although many of the publications associated with GenBank records may not be linked into or part of complementary literature databases (e.g., PubMed), GenBank records associated with literature indexed in Medline are identifiable as they contain PubMed identifiers (PMIDs). Results Here we show that an analysis of 87,116,501 GenBank sequence files reveals that 42% are associated with a publication or patent. Of these, 71% are associated with PMIDs, and can therefore be linked to a citation record in the PubMed database. The remaining (29%) of publication-associated GenBank entries either do not have PMIDs or cite a publication that is not currently indexed by PubMed. We also identify the journal titles that are linked through citations in the GenBank files to the largest number of sequences. Conclusion Our analysis suggests that GenBank contains molecular sequences from a range of disciplines beyond biomedicine, the initial scope of PubMed. The findings thus suggest opportunities to develop mechanisms for integrating biological knowledge beyond the biomedical field.

Miller, Holly; Norton, Catherine N; Sarkar, Indra Neil

2009-01-01

61

76 FR 28973 - Terra-Gen Dixie Valley, LLC; Order on Rehearing and Accepting Tariff Filing, Subject to...  

Federal Register 2010, 2011, 2012, 2013

...addressed a complaint filed against Terra- Gen by Green Borders Geothermal, LLC (Green Borders). In relevant part, the Commission found...Terra-Gen must file an OATT as a result of Green Borders' valid transmission service request...

2011-05-19

62

The influence of gender, social cause, charitable support, and message appeal on Gen Y's responses to cause-related marketing  

Microsoft Academic Search

This study examined the influence of gender, type of social cause, amount of charitable support, and message appeal on Gen Y consumers' attitudes and purchase intentions towards an apparel brand within the context of cause-related marketing. A questionnaire, with an experimental design component, was administered to a sample of 562 Gen Y college students. Results suggest that Gen Y consumers

Karen H. Hyllegard; Ruoh-Nan Yan; Jennifer Paff Ogle; Julianne Attmann

2010-01-01

63

Decay heat removal in GEN IV gas cooled fast reactors.  

SciTech Connect

The safety goal of the current designs of advanced high-temperature thermal gas-cooled reactors (HTRs) is that no core meltdown would occur in a depressurization event with a combination of concurrent safety system failures. This study focused on the analysis of passive decay heat removal (DHR) in a GEN IV direct-cycle gas-cooled fast reactor (GFR) which is based on the technology developments of the HTRs. Given the different criteria and design characteristics of the GFR, an approach different from that taken for the HTRs for passive DHR would have to be explored. Different design options based on maintaining core flow were evaluated by performing transient analysis of a depressurization accident using the system code RELAP5-3D. The study also reviewed the conceptual design of autonomous systems for shutdown decay heat removal and recommends that future work in this area should be focused on the potential for Brayton cycle DHRs.

Cheng, L. Y.; Wei, T. Y. C. (Nuclear Engineering Division); (BNL)

2009-08-01

64

Kriegella aquimaris gen. nov., sp. nov., isolated from marine environments.  

PubMed

Two novel marine, heterotrophic, gliding, Gram-negative, aerobic and orange-pigmented strains were investigated by using a polyphasic approach. 16S rRNA gene sequence analysis indicated an affiliation of the novel isolates to the family Flavobacteriaceae of the phylum Bacteroidetes. The level of sequence similarity between the strains studied and their closest relatives, the recognized Zobellia species, ranged from 93.2 to 93.9 %. Phylogenetic evidence, supported by several differences in phenotypic characteristics between the novel isolates and Zobellia species such as the absence of nitrate reductase, agarase and gelatinase activities together with the ability to produce acid from galactose, lactose and melibiose, allowed their assignment to a new genus and species, for which the name Kriegella aquimaris gen. nov., sp. nov. is proposed. The type strain of Kriegella aquimaris is KMM 3665(T) (=KCTC 22188(T) =DSM 19886(T)). PMID:18984704

Nedashkovskaya, Olga I; Suzuki, Makoto; Kim, Seung Bum; Mikhailov, Valery V

2008-11-01

65

Two-dimensional MHD generator model. [GEN code  

SciTech Connect

A steady state, two-dimensional MHD generator code, GEN, is presented. The code solves the equations of conservation of mass, momentum, and energy, using a Von Mises transformation and a local linearization of the equations. By splitting the source terms into a part proportional to the axial pressure gradient and a part independent of the gradient, the pressure distribution along the channel is easily obtained to satisfy various criteria. Thus, the code can run effectively in both design modes, where the channel geometry is determined, and analysis modes, where the geometry is previously known. The code also employs a mixing length concept for turbulent flows, Cebeci and Chang's wall roughness model, and an extension of that model to the effective thermal diffusities. Results on code validation, as well as comparisons of skin friction and Stanton number calculations with experimental results, are presented.

Geyer, H.K.; Ahluwalia, R.K.; Doss, E.D.

1980-09-01

66

Hand-held optical imager (Gen-2): improved instrumentation and target detectability.  

PubMed

Hand-held optical imagers are developed by various researchers towards reflectance-based spectroscopic imaging of breast cancer. Recently, a Gen-1 handheld optical imager was developed with capabilities to perform two-dimensional (2-D) spectroscopic as well as three-dimensional (3-D) tomographic imaging studies. However, the imager was bulky with poor surface contact (~30%) along curved tissues, and limited sensitivity to detect targets consistently. Herein, a Gen-2 hand-held optical imager that overcame the above limitations of the Gen-1 imager has been developed and the instrumentation described. The Gen-2 hand-held imager is less bulky, portable, and has improved surface contact (~86%) on curved tissues. Additionally, the forked probe head design is capable of simultaneous bilateral reflectance imaging of both breast tissues, and also transillumination imaging of a single breast tissue. Experimental studies were performed on tissue phantoms to demonstrate the improved sensitivity in detecting targets using the Gen-2 imager. The improved instrumentation of the Gen-2 imager allowed detection of targets independent of their location with respect to the illumination points, unlike in Gen-1 imager. The developed imager has potential for future clinical breast imaging with enhanced sensitivity, via both reflectance and transillumination imaging. PMID:23224163

Gonzalez, Jean; Decerce, Joseph; Erickson, Sarah J; Martinez, Sergio L; Nunez, Annie; Roman, Manuela; Traub, Barbara; Flores, Cecilia A; Roberts, Seigbeh M; Hernandez, Estrella; Aguirre, Wenceslao; Kiszonas, Richard; Godavarty, Anuradha

2012-08-01

67

Use of experimental design to optimize docking performance: the case of LiGenDock, the docking module of LiGen, a new de novo design program.  

PubMed

On route toward a novel de novo design program, called LiGen, we developed a docking program, LiGenDock, based on pharmacophore models of binding sites, including a non-enumerative docking algorithm. In this paper, we present the functionalities of LiGenDock and its accompanying module LiGenPocket, aimed at the binding site analysis and structure-based pharmacophore definition. We also report the optimization procedure we have carried out to improve the cognate docking and virtual screening performance of LiGenDock. In particular, we applied the design of experiments (DoE) methodology to screen the set of user-adjustable parameters to identify those having the largest influence on the accuracy of the results (which ensure the best performance in pose prediction and in virtual screening approaches) and then to choose their optimal values. The results are also compared with those obtained by two popular docking programs, namely, Glide and AutoDock for pose prediction, and Glide and DOCK6 for Virtual Screening. PMID:23590204

Beato, Claudia; Beccari, Andrea R; Cavazzoni, Carlo; Lorenzi, Simone; Costantino, Gabriele

2013-04-30

68

Tools for Designing, Evaluating, and Certifying NextGen Technologies and Procedures: Automation Roles and Responsibilities.  

National Technical Information Service (NTIS)

Barbara Kanki from NASA Ames Research Center will discuss research that focuses on the collaborations between pilots, air traffic controllers and dispatchers that will change in NextGen systems as automation increases and roles and responsibilities change...

B. G. Kanki

2011-01-01

69

LiGen: a high performance workflow for chemistry driven de novo design.  

PubMed

Tools for molecular de novo design are actively sought incorporating sets of chemical rules for fast and efficient identification of structurally new chemotypes endowed with a desired set of biological properties. In this paper, we present LiGen, a suite of programs which can be used sequentially or as stand-alone tools for specific purposes. In its standard application, LiGen modules are used to define input constraints, either structure-based, through active site identification, or ligand-based, through pharmacophore definition, to docking and to de novo generation. Alternatively, individual modules can be combined in a user-defined manner to generate project-centric workflows. Specific features of LiGen are the use of a pharmacophore-based docking procedure which allows flexible docking without conformer enumeration and accurate and flexible reactant mapping coupled with reactant tagging through substructure searching. The full description of LiGen functionalities is presented. PMID:23617275

Beccari, Andrea R; Cavazzoni, Carlo; Beato, Claudia; Costantino, Gabriele

2013-05-28

70

78 FR 28940 - Ninth Meeting: RTCA Next Gen Advisory Committee (NAC)  

Federal Register 2010, 2011, 2012, 2013

...of Meeting and Introduction of NAC Members--Chairman Bill Ayer, Chairman, Alaska Air Group Official Statement of Designated...February 7, 2013 Meeting Summary Chairman's Report--Chairman Ayer FAA Report--Mr. Huerta FAA NextGen Performance...

2013-05-16

71

Market Withdrawal of HIV-1 / HCV Assay-Procleix - Gen-Probe ...  

Center for Biologics Evaluation and Research (CBER)

... Market Withdrawal of HIV-1 / HCV Assay-Procleix - Gen-Probe Inc. DATE WITHDRAWAL INITIATED: January 18, 2005. ... HIV-1 / HCV Assay, Procleix. ... More results from www.fda.gov/biologicsbloodvaccines/safetyavailability/recalls

72

76 FR 22162 - Third Meeting RTCA NextGen Advisory Committee (NAC)  

Federal Register 2010, 2011, 2012, 2013

...DEPARTMENT OF TRANSPORTATION Federal Aviation Administration Third Meeting RTCA NextGen Advisory Committee (NAC) AGENCY: Federal...Attendance is open to the interested public but limited to space availability. With the approval of the chairman, members...

2011-04-20

73

E-Gen: Automatic Job Offer Processing System for Human Resources  

Microsoft Academic Search

The exponential growth of the Internet has allowed the development of a market of on-line job search sites. This paper aims\\u000a at presenting the E-Gen system (Automatic Job Offer Processing system for Human Resources). E-Gen will implement two complex\\u000a tasks: an analysis and categorisation of job postings, which are unstructured text documents (e-mails of job listings possibly\\u000a with an attached

Rémy Kessler; Juan Manuel Torres Moreno; Marc El-bèze

2007-01-01

74

GenGED - A Visual Definition Tool for Visual Modeling Environments  

Microsoft Academic Search

\\u000a In this paper, we give a brief overview on GenGED that allows for the visual definition and generation of visual modeling\\u000a environments. Depending on the underlying visual modeling language, different components are suitable in a visual modeling\\u000a environment. GenGED supports the definition and generation of editors, parsers, and simulators.

Roswitha Bardohl; Claudia Ermel; Ingo Weinhold

2003-01-01

75

Genes and proteins of Escherichia coli K-12 (GenProtEC).  

PubMed

GenProtEC is a database of Escherichia coli genes and their gene products, classified by type of function and physiological role and with citations to the literature for each. Also present are data on sequence similarities amongE.coliproteins with PAM values, percent identity of amino acids, length of alignment and percent aligned. GenProtEC can also be accessed through the World Wide Web at URL http://mbl.edu/html/ecoli.html . PMID:9016503

Riley, M

1997-01-01

76

GenRev: exploring functional relevance of genes in molecular networks  

PubMed Central

We introduce GenRev, a network-based software package developed to explore the functional relevance of genes generated as an intermediate result from numerous high-throughput technologies. GenRev searches for optimal intermediate nodes (genes) for the connection of input nodes via several algorithms, including the Klein-Ravi algorithm, the limited kWalks algorithm and a heuristic local search algorithm. Gene ranking and graph clustering analyses are integrated into the package. GenRev has the following features. (1) It provides users with great flexibility to define their own networks. (2) Users are allowed to define each gene’s importance in a subnetwork search by setting its score. (3) It is standalone and platform independent. (4) It provides an optimization in subnetwork search, which dramatically reduces the running time. GenRev is particularly designed for general use so that users have the flexibility to choose a reference network and define the score of genes. GenRev is freely available at http://bioinfo.mc.vanderbilt.edu/GenRev.html.

Zheng, Siyuan; Zhao, Zhongming

2012-01-01

77

Anaerosporobacter mobilis gen. nov., sp. nov., isolated from forest soil.  

PubMed

A strictly anaerobic, Gram-positive, endospore-forming bacterium, strain HY-37-4(T), was isolated from a forest-soil sample collected in Jeju, Republic of Korea. The cells were motile rods with peritrichous flagella. Strain HY-37-4(T) fermented various carbohydrates and the end products from glucose were formate, acetate and H(2). The major cellular fatty acids were C(16 : 0), C(16 : 0) 3-OH and iso-C(17 : 1) I/anteiso B. The G+C content of the DNA was 41 mol%. A phylogenetic analysis based on 16S rRNA sequence data indicated that the forest isolate was most closely related to Clostridium herbivorans, Clostridium populeti, Clostridium polysaccharolyticum and Eubacterium xylanophilum, which belong to Clostridium cluster XIVa. However, the low levels of 16S rRNA gene sequence similarity (92.3-93.9 %) with respect to these taxa indicate that strain HY-37-4(T) represents a novel species. Several phenotypic characteristics readily allowed the isolate to be distinguished from other phylogenetically related taxa. On the basis of the polyphasic evidence, strain HY-37-4(T) represents a novel taxon, for which the name Anaerosporobacter mobilis gen. nov., sp. nov. is proposed. The type strain is HY-37-4(T) (=IMSNU 40011(T)=KCTC 5027(T)=DSM 15930(T)). PMID:17684257

Jeong, Hyunyoung; Lim, Young Woon; Yi, Hana; Sekiguchi, Yuji; Kamagata, Yoichi; Chun, Jongsik

2007-08-01

78

Modelling of advanced structural materials for GEN IV reactors  

NASA Astrophysics Data System (ADS)

The choice of suitable materials and the assessment of long-term materials damage are key issues that need to be addressed for the safe and reliable performance of nuclear power plants. Operating conditions such as high temperatures, irradiation and a corrosive environment degrade materials properties, posing the risk of very expensive or even catastrophic plant damage. Materials scientists are faced with the scientific challenge to determine the long-term damage evolution of materials under service exposure in advanced plants. A higher confidence in life-time assessments of these materials requires an understanding of the related physical phenomena on a range of scales from the microscopic level of single defect damage effects all the way up to macroscopic effects. To overcome lengthy and expensive trial-and-error experiments, the multiscale modelling of materials behaviour is a promising tool, bringing new insights into the fundamental understanding of basic mechanisms. This paper presents the multiscale modelling methodology which is taking root internationally to address the issues of advanced structural materials for Gen IV reactors.

Samaras, M.; Hoffelner, W.; Victoria, M.

2007-09-01

79

Critical Issues on Materials for Gen-IV Reactors  

SciTech Connect

Within the LDRD on 'Critical Issues on Materials for Gen-IV Reactors' basic thermodynamics of the Fe-Cr alloy and accurate atomistic modeling were used to help develop the capability to predict hardening, swelling and embrittlement using the paradigm of Multiscale Materials Modeling. Approaches at atomistic and mesoscale levels were linked to build-up the first steps in an integrated modeling platform that seeks to relate in a near-term effort dislocation dynamics to polycrystal plasticity. The requirements originated in the reactor systems under consideration today for future sources of nuclear energy. These requirements are beyond the present day performance of nuclear materials and calls for the development of new, high temperature, radiation resistant materials. Fe-Cr alloys with 9-12% Cr content are the base matrix of advanced ferritic/martensitic (FM) steels envisaged as fuel cladding and structural components of Gen-IV reactors. Predictive tools are needed to calculate structural and mechanical properties of these steels. This project represents a contribution in that direction. The synergy between the continuous progress of parallel computing and the spectacular advances in the theoretical framework that describes materials have lead to a significant advance in our comprehension of materials properties and their mechanical behavior. We took this progress to our advantage and within this LDRD were able to provide a detailed physical understanding of iron-chromium alloys microstructural behavior. By combining ab-initio simulations, many-body interatomic potential development, and mesoscale dislocation dynamics we were able to describe their microstructure evolution. For the first time in the case of Fe-Cr alloys, atomistic and mesoscale were merged and the first steps taken towards incorporating ordering and precipitation effects into dislocation dynamics (DD) simulations. Molecular dynamics (MD) studies of the transport of self-interstitial, vacancy and point defect clusters in concentrated Fe-Cr alloys were performed for future diffusion data calculations. A recently developed parallel MC code with displacement allowed us to predict the evolution of the defect microstructures, local chemistry changes, grain boundary segregation and precipitation resulting from radiation enhanced diffusion. We showed that grain boundaries, dislocations and free surfaces are not preferential for alpha-prime precipitation, and explained experimental observations of short-range order (SRO) in Fe-rich FeCr alloys. Our atomistic studies of dislocation hardening allowed us to obtain dislocation mobility functions for BCC pure iron and Fe-Cr and determine for FCC metals the dislocation interaction with precipitates with a description to be used in Dislocation Dynamic (DD) codes. A Synchronous parallel Kinetic Monte Carlo code was developed and tested which promises to expand the range of applicability of kMC simulations. This LDRD furthered the limits of the available science on the thermodynamic and mechanic behavior of metallic alloys and extended the application of physically-based multiscale materials modeling to cases of severe temperature and neutron fluence conditions in advanced future nuclear reactors. The report is organized as follows: after a brief introduction, we present the research activities, and results obtained. We give recommendations on future LLNL activities that may contribute to the progress in this area, together with examples of possible research lines to be supported.

Caro, M; Marian, J; Martinez, E; Erhart, P

2009-02-27

80

Electricity Generation Cost Simulation Model (GenSim).  

SciTech Connect

The Electricity Generation Cost Simulation Model (GenSim) is a user-friendly, high-level dynamic simulation model that calculates electricity production costs for variety of electricity generation technologies, including: pulverized coal, gas combustion turbine, gas combined cycle, nuclear, solar (PV and thermal), and wind. The model allows the user to quickly conduct sensitivity analysis on key variables, including: capital, O&M, and fuel costs; interest rates; construction time; heat rates; and capacity factors. The model also includes consideration of a wide range of externality costs and pollution control options for carbon dioxide, nitrogen oxides, sulfur dioxide, and mercuty. Two different data sets are included in the model; one from the US. Department of Energy (DOE) and the other from Platt's Research Group. Likely users of this model include executives and staff in the Congress, the Administration and private industry (power plant builders, industrial electricity users and electric utilities). The model seeks to improve understanding of the economic viability of various generating technologies and their emissions trade-offs. The base case results, using the DOE data, indicate that in the absence of externality costs, or renewable tax credits, pulverized coal and gas combined cycle plants are the least cost alternatives at 3.7 and 3.5 cents/kwhr, respectively. A complete sensitivity analysis on fuel, capital, and construction time shows that these results coal and gas are much more sensitive to assumption about fuel prices than they are to capital costs or construction times. The results also show that making nuclear competitive with coal or gas requires significant reductions in capital costs, to the $1000/kW level, if no other changes are made. For renewables, the results indicate that wind is now competitive with the nuclear option and is only competitive with coal and gas for grid connected applications if one includes the federal production tax credit of 1.8cents/kwhr.

Kamery, William (Hobart and William Smith Colleges, Geneva, NY); Baker, Arnold Barry; Drennen, Thomas E.

2003-07-01

81

Tamlicoccus marinus gen. nov., sp. nov., isolated from seawater.  

PubMed

A novel actinobacterial strain was isolated from a seawater sample collected on Mara Island, Jeju, Republic of Korea. Cells of this organism were aerobic, Gram-positive, non-spore-forming, non-motile cocci that occurred singly or in pairs. Colonies were circular, smooth, convex and white-cream in colour. Phylogenetic analyses based on 16S rRNA gene sequences showed that the organism belonged to the family Dermacoccaceae and formed a monophyletic clade between the type strains of Demetria terragena (96.8% similarity) and Branchiibius hedensis (95.2% similarity). The cell-wall peptidoglycan contained L-lysine, alanine, aspartic acid, glutamic acid, glycine and serine, indicating that the isolate possessed peptidoglycan type A4?. The whole-cell sugars were galactose, glucose, mannose, xylose, arabinose, ribose and rhamnose. The major menaquinone was MK-8(H4). The polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, an unknown phospholipid and five unknown lipids. The cellular fatty acid profile was represented by large amounts of iso-methyl branched and monounsaturated iso- and anteiso-methyl branched acids, along with the presence of a diagnostic 10-methyl acid. The G+C content of the DNA was 71 mol%. On the basis of data from polyphasic analyses presented here, strain MSW-24(T) is considered to represent a novel species of a new genus in the family Dermacoccaceae, for which the name Tamlicoccus marinus gen. nov., sp. nov. is proposed. The type strain of Tamlicoccus marinus is MSW-24(T) (=KCTC 19485(T)=DSM 21415(T)). PMID:23041643

Lee, Soon Dong

2012-10-05

82

Rudaibacter terrae gen. nov., sp. nov., isolated from greenhouse soil.  

PubMed

One novel Gram-stain-positive, non-motile, rod-shaped bacterium, designated 5GHs34-4T, was isolated from greenhouse soil in Yongin, Republic of Korea. Growth occurred in the range of 10-37 °C (optimum 28-30 °C) and pH 5.0-9.0 (optimum pH 7.0). It can tolerate up to 3?% (w/v) NaCl. The strain showed 16S rRNA gene sequence similarity levels of 95.1-97.0% with Leifsonia species, 95.7-96.7% with Herbiconiux species, 95.1-96.4% with Salinibacterium species, and 96.1% with Labedella gwakjiensis and Homoserinimonas aerilata. The highest sequence similarities (97.0%) were shown with Leifsonia aquatica JCM 1368T, Leifsonia poae VKM Ac-1401T and Leifsonia psychrotolerans LI1T. The peptidoglycan type determined for strain 5GHs34-4T was B2? with DL-2,4-diaminobutyric acid at the position 3. The murein was of the acetyl type. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol and two unknown glycolipids. The menaquinones detected were MK-13, MK-12 and MK-14, and the major fatty acids were summed feature 8 (C18:1 ?7c and/or C18:1 ?6c), anteiso-C17:0 and anteiso-C15:0. The phenotypic and phylogenetic traits of strain 5GHs34-4T differed in some respects from those of members of the family Microbacteriaceae. Therefore, strain 5GHs34-4T is considered to represent a novel species of a new genus in the family Microbacteriaceae, for which the name Rudaibacter terrae gen. nov., sp. nov. is proposed. The type strain is 5GHs34-4T (?= KACC 15523T = NBRC 108754T). PMID:23728372

Kim, Soo-Jin; Moon, Ji-Young; Hamada, Moriyuki; Tamura, Tomohiko; Weon, Hang-Yeon; Suzuki, Ken-Ichiro; Kwon, Soon-Wo

2013-05-31

83

Falsochrobactrum ovis gen. nov., sp. nov., isolated from a sheep.  

PubMed

A Gram-stain-negative, rod-shaped, oxidase-positive, non-spore-forming, non-motile bacterium (B1315(T)) was isolated from the placenta of a sheep with abortion. On the basis of 16S rRNA gene sequence analyses the strain was assigned to the Brucella-Ochrobactrum-Paenochrobactrum-Pseudochrobactrum group with 94.5-94.8?%, 94.3-96.1?%, 95.0-95.1?%, and 95.9-96.1?% sequence similarities to type strains of species of the four genera, respectively. Phylogenetic trees indicated a close relationship to the type strains of Ochrobactrum gallinifaecis and Ochrobactrum oryzae (95.9 and 96.1?% sequence similarity, respectively). Chemotaxonomic data confirmed the allocation of strain B1315(T) to the family Brucellaceae (quinone system: ubiquinone Q-10 and major fatty acids: C18?:?1?7c and C19?:?0 cyclo ?8c). The polar lipid profile contained the major lipids diphosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and the unidentified but unique phospholipid PL7. The polyamine pattern of strain B1315(T) contained the major polyamines spermidine and putrescine. On the basis of the 16S rRNA gene and recA sequence phylogeny and chemotaxonomic data strain B1315(T) was clearly different from the genera Brucella, Ochrobactrum, Paenochrobactrum and Pseudochrobactrum. On the basis of these data we propose the novel genus Falsochrobactrum gen. nov. with the type species Falsochrobactrum ovis sp. nov. with the type strain B1315(T) (?=?CCM 8460(T)?=?LMG 27356(T.)) The taxonomic allocation of O. gallinifaecis, which grouped inconsistently together with strain B1315(T) on the basis of 16S rRNA gene sequence data, but shows the chemotaxonomic features of the genus Ochrobactrum, remains to be clarified. PMID:23687057

Kämpfer, Peter; Glaeser, Stefanie; Busse, Hans-Jürgen; Eisenberg, Tobias; Scholz, Holger

2013-05-17

84

Fusicatenibacter saccharivorans gen. nov., sp. nov., isolated from human faeces.  

PubMed

Three Gram-stain-positive, obligately anaerobic, non-motile, non-spore-forming, spindle-shaped bacterial strains (HT03-11(T), KO-38 and TT-111), isolated from human faeces were characterized by phenotypic and molecular taxonomic methods. Comparative 16S rRNA gene sequencing showed that the strains were highly related to each other genetically (displaying >99?% sequence similarity) and represented a previously unknown subline within the Blautia coccoides rRNA group of organisms (cluster XIVa). The closest phylogenetic neighbours of strain HT03-11(T) were Clostridium bolteae WAL 16351(T) (93.7?% 16S rRNA gene sequence similarity) and Clostridium saccharolyticum WM1(T) (93.7?% similarity). All isolates produced lactic acid, formic acid, acetic acid and succinic acid as fermentation end products from glucose. Their chemotaxonomic properties included lysine as the cell wall diamino acid and C16?:?0, C18?:?1?7c DMA and C16?:?0 DMA as the major fatty acids. The G+C contents of the genomic DNA were 46.9-47.2 mol% (HPLC). Several phenotypic and chemotaxonomic characteristics could be readily used to differentiate the isolates from phylogenetically related clostridia. Therefore, strains HT03-11(T), KO-38 and TT-111 represent a novel species in a new genus of the family Lachnospiraceae, for which the name Fusicatenibacter saccharivorans gen. nov., sp. nov. is proposed. The type strain of the type species is HT03-11(T) (?=?YIT 12554(T)?=?JCM 18507(T)?=?DSM 26062(T)). PMID:23625266

Takada, Toshihiko; Kurakawa, Takashi; Tsuji, Hirokazu; Nomoto, Koji

2013-04-26

85

Muriicola jejuensis gen. nov., sp. nov., isolated from seawater.  

PubMed

An aerobic, yellow-orange-pigmented, Gram-staining-negative bacterium, designated strain EM44(T), was isolated from seawater on the eastern coast of Jeju Island, Korea. Growth was observed at 15-35 degrees C (optimum 25-30 degrees C), pH 6.5-9.0 (optimum pH 7.0-8.5) and between 1 and 5 % NaCl (w/v) (optimum 2-4 %). Cells of strain EM44(T) were non-motile, straight rods and showed catalase and oxidase activities. The G+C content of the genomic DNA was 47.9 mol% and the major respiratory quinone was MK-6. The major fatty acids were iso-C(15 : 0) G, iso-C(15 : 0), iso-C(17 : 0) 3-OH and iso-C(16 : 0) 3-OH. Strain EM44(T) contained phosphatidylethanolamine as a major polar phospholipid. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain EM44(T) fell within the family Flavobacteriaceae in the phylum Bacteroidetes and was most closely related to members of the genera Eudoraea, Zeaxanthinibacter and Robiginitalea with 92-94.5 % gene sequence similarities. On the basis of chemotaxonomic data and molecular properties, it is clear that strain EM44(T) represents a novel genus within the family Flavobacteriaceae, for which the name Muriicola jejuensis gen. nov., sp. nov. is proposed. The type strain of the type species is EM44(T) (=KCTC 22299(T)=DSM 21206(T)). PMID:19717580

Kahng, Hyung-Yeel; Lee, Sang-Suk; Kim, Jeong Myeong; Jung, Ji Young; Lee, Mee Young; Park, Woojun; Jeon, Che Ok

2009-08-28

86

GenBank at Los Alamos: User manual, training guide, and reference manual for the ASCII AWB  

Microsoft Academic Search

The GenBank project at Los Alamos collects nucleotide sequence submissions from the biological research community. This work includes the processing of data received in several different forms as well as maintenance and quality control on those submissions. This manual explains the procedures involved in that work for both Los Alamos GenBank staff and off-site users. The GenBank database stores annotated

G. C. Reese; G. M. Keen; P. Gilna; M. J. Cinkosky

1993-01-01

87

GenBank at Los Alamos: User manual, training guide, and reference manual for the OPEN LOOK[trademark] AWB  

Microsoft Academic Search

The GenBank project at Los Alamos collects nucleotide sequence submissions from the biological research community. This work includes the processing of data received in several different forms as well as maintenance and quality control on those submissions. This manual explains the procedures involved in that work for both Los Alamos GenBank staff and off-site users. The GenBank database stores annotated

G. C. Reese; G. M. Keen; P. Gilna; M. J. Cinkosky

1993-01-01

88

Halobellus clavatus gen. nov., sp. nov. and Halorientalis regularis gen. nov., sp. nov., two new members of the family Halobacteriaceae.  

PubMed

Four halophilic archaeal strains, designated TNN18(T), TBN12, TNN28(T) and TBN19, were isolated from brines sampled from two artificial marine solar salterns in eastern China. Strains TNN18(T) and TNN28(T) were isolated from the Tainan marine solar saltern, whereas strains TBN12 and TBN19 were from the Taibei marine solar saltern. Colonies of the four strains were red-pigmented and their cells were pleomorphic, motile, Gram-reaction-negative rods. Strains TNN18(T) and TBN12 were able to grow at 25-50 °C (optimum 37 °C), in 10-3 ?% (w/v) NaCl (optimum 15 %), with 0-1.0 M MgCl(2) (optimum 0.05 M) and at pH 5.5-9.0 (optimum pH 7.0-7.5), while strains TNN28(T) and TBN19 were able to grow at 20-50 °C (optimum 37 °C), in 15-30 % (w/v) NaCl (optimum 18-20 %), in 0.005-1.0 M MgCl(2) (optimum 0.01-0.3 M) and at pH 6.0-9.0 (optimum pH 7.0-7.5). Cells of these strains lyse in distilled water; minimal NaCl concentrations to prevent cell-lysis are 10?% (w/v) for strains TNN18(T) and TBN12 and 12 % (w/v) for strains TNN28(T) and TBN19. The major polar lipids of strains TNN18(T) and TBN12 were phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me), phosphatidylglycerol sulfate (PGS) and one major glycolipid (GL1), which was chromatographically identical to sulfated mannosyl glucosyl diether (S-DGD-1). Minor amounts of other lipids (GL0, GL2, GL3 and GL4) were also detectable. The polar lipid profiles of strains TNN28(T) and TBN19 contained PG, PGP-Me, GL1, which was chromatographically identical to S-DGD-1, and three to four minor unidentified glycolipids (GL2-GL5). Phylogenetic analyses revealed that strains TNN18(T) and TBN12 formed a distinct clade with strains of the closest related species, Haloquadratum walsbyi (91.5-91.8 % 16S rRNA gene sequence similarity) and strains TNN28(T) and TBN19 formed a distinct clade with strains of the species Halosimplex carlsbadense (89.9-93.3 % similarity) and two members of the genus Halorhabdus (92.5-93.3 % similarity). The DNA G+C contents of strains TNN18(T), TBN12, TNN28(T) and TBN19 were 61.5, 62.4, 61.9 and 61.5 mol%, respectively. DNA-DNA hybridization values between strains TNN18(T) and TBN12, and strains TNN28(T) and TBN19 were 82.9 % and 88.2 %, respectively. The phenotypic, chemotaxonomic and phylogenetic properties suggest that the four strains represent two novel species of two new genera within the family Halobacteriaceae, for which the names Halobellus clavatus gen. nov., sp. nov. (type strain TNN18(T ) = CGMCC 1.10118(T ) = JCM 16424(T)) and Halorientalis regularis gen. nov., sp. nov. (type strain TNN28(T ) = CGMCC 1.10123(T ) = JCM 16425(T)) are proposed. PMID:21169458

Cui, Heng-Lin; Yang, Xin; Gao, Xia; Xu, Xue-Wei

2010-12-17

89

Correlation between ORange® (Gen 1, pseudophakic) intraoperative refraction and 1-week postcataract surgery autorefraction  

PubMed Central

Background: This study aimed to find the strength of the correlation between ORange® (intraoperative wavefront aberrometer) objective refraction during pseudophakic cataract surgery (Gen 1) and 1-week objective autorefraction postcataract surgery in order to establish the clinical degree of confidence in the ORange. Gen 1 was used because Gen 2 was not available at the time of the study. However, Gen 1 can still be a good reference. Methods: Thirty-two consecutive eyes were included in this prospective nonrandomized study. ORange was used after phacoemulsification and intraocular lens implantation. There were no complications and no withdrawals from the study. The refraction data from the ORange were recorded in spherical equivalents and put into Excel. One week postoperatively, autorefraction was done and the data were again recorded in spherical equivalents and put into Excel. Both sets of data were then transferred to SPSS for a correlation study. Because ORange is an objective refractor, it is necessary to use another objective refractor, such as the Zeiss Autorefractor, for comparison. Measurement at 1 week postoperatively is for cornea clearance for autorefraction and is the closest time to intraoperative assessment for comparison. Results: The Pearson correlation was r = +0.56, P < 0.01, which qualifies for a moderate or good correlation (0.5–0.75). Conclusion: Intraoperative refraction using the ORange Gen 1 after cataract surgery and intraocular lens implantation is moderate to good when correlated with objective autorefraction 1 week after cataract surgery.

Chen, Ming

2011-01-01

90

HIV gp120 vaccine - VaxGen: AIDSVAX, AIDSVAX B/B, AIDSVAX B/E, HIV gp120 vaccine - Genentech, HIV gp120 vaccine AIDSVAX - VaxGen, HIV vaccine AIDSVAX - VaxGen.  

PubMed

VaxGen is developing prophylactic vaccines against HIV-1 consisting of two recombinant gp120 surface proteins from different HIV-1 strains.This profile has been selected from R&D Insight, a pharmaceutical intelligence database produced by Adis International Ltd. The bivalent vaccines [AIDSVAX B/B and AIDSVAX B/E] are being evaluated in two phase III trials. The first multicentre phase III trial of AIDSVAX B/B, was conducted principally in Canada and the US but also at some sites in the Netherlands and Puerto Rico. The trial was completed at the end of 2002. The second phase III trial is being conducted in Thailand with the AIDSVAX B/E vaccine. VaxGen announced in July 2002 that it would be delaying its Biologics License Application (BLA) for AIDSVAX until 2004 to enable the company to fulfil pre-approval manufacturing requirements. AIDSVAX is based on an earlier monovalent gp120 vaccine developed by Genentech that was shown to be safe in humans. VaxGen (formerly Genenvax) was formed as a spin-off company from Genentech with the sole purpose of developing the gp120 vaccine. VaxGen announced in July 2002 that the original License and Supply agreement with Genentech, signed in May 1997, had been amended. Under the revised agreement, Genentech maintains its right to market and sell AIDSVAX in North America, but has relinquished its options to commercialise the vaccine candidate in the rest of the world. Genentech's earlier decision to waive its option to manufacture AIDSVAX has also been formalised in this agreement. Additionally, VaxGen's royalty payments to Genentech for sales to the WHO or UN for underdeveloped nations have also been reduced by up to 50% and Genentech has extended the milestone date associated with VaxGen submitting an NDA. A $US120 million joint venture (Celltrion) has been formed between VaxGen and South Korean investors to manufacture more than 200 million doses of AIDSVAX a year. Celltrion will build and operate two biotechnology manufacturing facilities: a pilot plant in South San Francisco and a larger plant in Incheon, South Korea. VaxGen will retain a 44% interest in the new company, as well as any profit generated by the AIDS vaccine. If AIDSVAX wins regulatory approval, VaxGen is committed to purchasing a minimum of 87 million doses a year. Celltrion announced in July 2002 that it had acquired 24 acres of land in Incheon, South Korea, for the site of its major biologics manufacturing facility. The facility is scheduled to be ready for commercial operation by 2005. The US FDA granted fast-track designations to the two vaccines AIDSVAX B/B and AIDSVAX B/E in December 2002. The study volunteers included 5108 men who have sex with men and 309 at-risk women, all of whom were meant to be HIV negative when they joined the trial. During the 36-month trial, a total of seven injections were administered at months 0, 1, 6, 12, 18, 24 and 30. The ratio of vaccine to placebo recipients was 2:1. On February 24 2003, VaxGen announced that AIDSVAX B/B did not prove effective in the trials conducted in North America and Europe. The study did not show a statistically significant reduction of HIV infection within the study population as a whole, which was the primary endpoint of the trial. However, the study did show a statistically significant reduction of HIV infection in certain vaccinated groups. Trial data indicate that black and Asian volunteers appeared to produce higher levels of antibodies against HIV. White and Hispanic volunteers appeared to develop consistently lower levels of protective antibodies following vaccination. VaxGen intends to conduct additional analyses to confirm if there was a direct correlation between the level of antibodies and the prevention of infection. The company intends to continue development of the vaccine through licensure, including any studies necessary to evaluate the protective riticism in the media about the statistical analysis of the non-Caucasian data, VaxGen issued a statement on 27 February 2003 claiming that the analysis of data from the trial followed a statistica

2003-01-01

91

Predatory behaviour of the social orb-weaver spider, Geratonephila burmanica n. gen., n. sp. (Araneae: Nephilidae) with its wasp prey, Cascoscelio incassus n. gen., n. sp. (Hymenoptera: Platygastridae) in Early Cretaceous Burmese amber  

Microsoft Academic Search

The present work shows predatory behaviour of the social orb-weaver spider, Geratonephila burmanica n. gen., n. sp. (Araneae: Nephilidae) against a parasitic wasp, Cascoscelio incassus n. gen., n. sp. (Hymenoptera: Platygastridae) in Early Cretaceous Burmese amber. An adult male and juvenile of G. burmanica in the same web provide the first fossil evidence of sociality in spiders. The spider is

George Poinar Jr; Ron Buckley

2011-01-01

92

Non contiguous-finished genome sequence and description of Senegalemassilia anaerobia gen. nov., sp. nov.  

PubMed Central

Senegalemassilia anaerobia strain JC110T sp.nov. is the type strain of Senegalemassilia anaerobia gen. nov., sp. nov., the type species of a new genus within the Coriobacteriaceae family, Senegalemassilia gen. nov. This strain, whose genome is described here, was isolated from the fecal flora of a healthy Senegalese patient. S. anaerobia is a Gram-positive anaerobic coccobacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,383,131 bp long genome contains 1,932 protein-coding and 58 RNA genes.

Lagier, Jean-Christophe; Elkarkouri, Khalid; Rivet, Romain; Couderc, Carine; Raoult, Didier; Fournier, Pierre-Edouard

2013-01-01

93

Non contiguous-finished genome sequence and description of Senegalemassilia anaerobia gen. nov., sp. nov.  

PubMed

Senegalemassilia anaerobia strain JC110(T) sp.nov. is the type strain of Senegalemassilia anaerobia gen. nov., sp. nov., the type species of a new genus within the Coriobacteriaceae family, Senegalemassilia gen. nov. This strain, whose genome is described here, was isolated from the fecal flora of a healthy Senegalese patient. S. anaerobia is a Gram-positive anaerobic coccobacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,383,131 bp long genome contains 1,932 protein-coding and 58 RNA genes. PMID:24019984

Lagier, Jean-Christophe; Elkarkouri, Khalid; Rivet, Romain; Couderc, Carine; Raoult, Didier; Fournier, Pierre-Edouard

2013-02-25

94

Discourses in Conflict: The Relationship between Gen Y Pre-Service Teachers, Digital Technologies and Lifelong Learning  

ERIC Educational Resources Information Center

|This paper analyses Gen Y pre-service primary school teachers' conceptualisations of lifelong learning. It is situated within a context of improving the provision and delivery of pre-service teacher education. This paper argues that Gen Y's understanding of lifelong learning has been influenced by their engagements with digital technologies and…

Donnison, Sharn

2009-01-01

95

Considerations of Alloy 617 Application in the Gen IV Nuclear Reactor Systems - Part I: Mechanical Property Challenges  

Microsoft Academic Search

Alloy 617 is currently considered as a leading candidate material for high temperature components in the Gen IV Nuclear Reactor Systems. Because of the unprecedented severe working conditions beyond its commercial service experience required by the Gen IV systems, the alloy faces various challenges in both mechanical and metallurgical properties. This paper, as Part I of the discussion, is focused

Weiju

2010-01-01

96

Considerations of Alloy 617 Application in the Gen IV Nuclear Reactor Systems - Part II: Metallurgical Property Challenges  

Microsoft Academic Search

Alloy 617 is currently considered as a leading candidate material for high temperature components in the Gen IV Nuclear Reactor Systems. Because of the unprecedented severe working conditions beyond its commercial service experience required by the Gen IV systems, the alloy faces various challenges in both mechanical and metallurgical properties. Following a previous paper discussing the mechanical property challenges, this

Weiju

2010-01-01

97

Complete cDNAs from Nylanderia sp. nr. pubens (Hymenoptera: Formicidae). GenBank GU980916-GU980928.  

Technology Transfer Automated Retrieval System (TEKTRAN)

13 new gene sequences were identified from workers of Rasberry crazy ant, Nylanderia sp.nr. pubens, and submitted to the National Center for Biotechnology Information GenBank. GenBank accession numbers are GU980916-GU980928. This information will provide scientists with genetic tools to study the p...

98

Mining metadata from unidentified ITS sequences in GenBank: A case study in Inocybe (Basidiomycota)  

Microsoft Academic Search

BACKGROUND: The lack of reference sequences from well-identified mycorrhizal fungi often poses a challenge to the inference of taxonomic affiliation of sequences from environmental samples, and many environmental sequences are thus left unidentified. Such unidentified sequences belonging to the widely distributed ectomycorrhizal fungal genus Inocybe (Basidiomycota) were retrieved from GenBank and divided into species that were identified in a phylogenetic

Martin Ryberg; R Henrik Nilsson; Erik Kristiansson; Mats Töpel; Stig Jacobsson; Ellen Larsson

2008-01-01

99

Distribution, paleoecology, paleoclimatology, and botanical affinity of the Eocene pollen genus Diporoconia n. gen  

Microsoft Academic Search

Diporoconia n. gen. is proposed for diporate subisopolar smooth to perforate pollen grains having annuli or tumescence. Diporoconia iszkaszentgyoergyi (Kedves) n. comb. (the type species), D. nnewiensis (Jan du Chêne et al.) n. comb., and D. spp. 1 and 2 are included in the genus. Distinctive characters of the pollen are the large pores that are at the ends of

N. O. Frederiksen; V. D. Wiggins; I. K. Ferguson; J. Dransfield; C. M. Ager

1985-01-01

100

Integrated Design and Production Reference Integration with ArchGenXML V1.00.  

National Technical Information Service (NTIS)

ArchGenXML is a tool that allows easy creation of Zope products through the use of Archetypes. The Integrated Design and Production Reference (IDPR) should be highly configurable in order to meet the needs of a diverse engineering community. Ease of confi...

R. H. Barter

2004-01-01

101

Integration framework for NASA NextGen Volumetric Cockpit Situation Display with haptic feedback  

Microsoft Academic Search

In this paper, we present a framework for the integration of force feedback information in a NASA NextGen Volumetric Cockpit Situation Display (CSD). With the current CSD, the user retrieves operational information solely through visual displays and interacts with the CSD tools through using a mouse. The advanced capabilities of the CSD may require complex manipulation of information which may

Jose Robles; Matthew Sguerri; R. Conrad Rorie; Kim-Phuong Vu; Thomas Z. Strybel; Panadda Marayong

2012-01-01

102

Two new Stratiomyinae, including Panamamyia gen. nov., from the Neotropical Region (Diptera: Stratiomyidae)  

Technology Transfer Automated Retrieval System (TEKTRAN)

A new species of Hoplitimyia James, H. inbioensis sp. nov., is described from Costa Rica. A new genus, Panamamyia gen. nov., with type species P. silbergliedi sp. nov., is described from Panama. Both taxa are very rare in collections, not having been taken during extensive Malaise trap surveys in ...

103

Thaumamermis cosgrovei n. gen., n. sp. (Mermithidae: Nematoda) parasitizing terrestrial isopods (Isopoda: Oniscoidea)  

Microsoft Academic Search

Summary  A new mermithid nematode, Thaumamermis cosgrovei n. gen., n. sp. (Mermithidae: Nematoda) was found parasitizing two terrestrial isopods (Isopoda: Oniscoidea) in California. The hosts, Armadillidium vulgare (Latr.) (a pillbug) and Porcellio scaber (Latr.) (a sowbug) represent the first cases of isopods attacked by mermithid nematodes. The genus Thaumamermis can be distinguished from all previously described mermithids by the extremely dimorphic

George O. Poinar

1981-01-01

104

Single phase permanent-magnet generator with low armature reaction for induction heating gen sets  

Microsoft Academic Search

The paper presents a single phase, slotless axial flux permanent magnet synchronous machine for induction heating gen sets. A full scale prototype of the machine (110 kVA, 400 Hz, 690 A) has been designed and subsequently analyzed through FEM analysis (FEA). Induced current distributions in the permanent magnets (PMs) and in the rotors are also calculated through FEA and it

F. Caricchi; F. Maradei; G. De Donato; F. Giulii Capponi

2008-01-01

105

Reclassification of Cellulomonas cellulans (Stackebrandt and Keddie 1986) as Cellulosimicrobium cellulans gen. nov., comb. nov  

Microsoft Academic Search

Phylogenetic analysis of 16S rDNA provides evidence that Cellulomonas cellulans branches outside the phylogenetic confines of the genus Cellulomonas. The distinct phylogenetic and chemotaxonomic status of Cellulomonas cellulans as a phylogenetic neighbour of the genus Promicromonospora, justifies the description of a new genus for which the name Cellulosimicrobium gen. nov. with the type species Cellulosimicrobium cellulans comb. nov. is proposed.

Peter Schumann; Norbert Weiss; Erko Stackebrandt

106

Gen Y Goes to College: Perceptions of High School Students and the Graduate Students They Mentored  

Microsoft Academic Search

This paper describes the perceptions and attitudes of high school students and the graduate students they assisted during a university multimedia class. Gen Y focuses on today's youth, enabling them to become contributing partners - and often leaders - in bringing technology into classrooms and communities. This project encouraged authentic participation of high school students as collaborative partners with graduate

Alice Christie; Valerie Naish; Jayme Kelter; Joey Wycoff; Cory Pearman; Jason Gender

107

Preliminary Considerations of Modified 9Cr1Mo Steel for Gen IV Nuclear Reactor Application  

Microsoft Academic Search

Modified 9Cr-1Mo steel is currently identified as one of the leading candidate materials in the down selection for construction of the Gen IV nuclear reactor pressure vessel. Because of the stringent requirements in strength, size, safety, design life, and maintenance for the intended nuclear application, qualification of the material demands scrutiny in various aspects such as mechanical properties, data sufficiency,

Weiju

2008-01-01

108

Proleptonchoides southindiae n. gen., n. sp., a New Leptonchoid from South India.  

PubMed

Proleptonchoides southindiae n. gen., n. sp. (Dorylaimida: Leptonchidae), is described from soil around false tobacco (Lobelia excelsa) and cardamom (Elettaria cardamomurn) in South India. P. southindiae is prodelphic, has a short constricted esophageal bulb and flanged odontophore, and is phylogenetically close to Proleptonchus. PMID:19305531

Ferris, V R; Goseco, C G; Kumar, A C

1979-01-01

109

Dayao gen. n. of the subtribe Tyrina (Coleoptera, Staphylinidae, Pselaphinae) from South China  

PubMed Central

Abstract Dayao pengzhongi gen. et sp. n. is described and illustrated based on the material collected in Guangxi Province, South China. The genus is placed in the oriental ‘Pselaphodes complex’ of genera of the subtribe Tyrina and its taxonomic placement is discussed.

Yin, Zi-Wei; Li, Li-Zhen; Zhao, Mei-Jun

2011-01-01

110

Anindobothrium N. Gen. (Eucestoda: Tetraphyllidea) Inhabiting Marine and Freshwater Potamotrygonid Stingrays  

Microsoft Academic Search

Anindobothrium n. gen. is proposed to accommodate Caulobothrium anacolum inhabiting Himantura schmardae from Colombia, and 2 new species, one inhabiting Potamotrygon orbignyin Brazil and the other inhabiting Paratrygon aereiba in Venezuela. Members of the new genus resemble members of Pararhinebothroides, Rhinebothroides,and Anthocephalum by having bothridia with poorly differentiated apical suckers and vasa deferentia expanded into external seminal vesicles. It further

FERNANDO P. L. MARQUES; DANIEL R. BROOKS; CARLOS A. LASSO

2001-01-01

111

Cathetocephalus thatcheri gen. et sp. n. (Tetraphyllidea: Cathetocephalidae) fam. n. from the Bull Shark  

Microsoft Academic Search

Cathetocephalus thatcheri gen. et sp. n. is described from the spiral valve of the bull shark, Carcharhinus leucas (Valenciennes), taken in the Gulf of Mexico and the Atlantic coast of Florida. A new family is erected for the new genus. The species most closely resembles Pillersium owenium Southwell, 1927, in that both possess a scolex which is perpendicular to the

Murray D. Dailey; Robin M. Overstreet

1973-01-01

112

Tricholimnichus gen.n. and three new species from Borneo (Coleoptera: Limnichidae)  

Microsoft Academic Search

Tricholimnichus gen.n. (Coleoptera: Limnichidae) and three new species, T. maior sp.n., T. sabahensis sp.n. and T. minor sp.n., are described from the island of Borneo (Oriental Region). The new genus seems to be closely related to the Afrotropical Cyclolimnichus DELÈVE.

C. HERN ANDÒ; I. RIBERA

113

Increasing airport arrival capacity in NextGen with wake turbulence avoidance  

Microsoft Academic Search

Arrival capacity at major airports is a primary constraint that must be overcome to reach the Next Generation Air Transportation System (NextGen) capacity goals. At the nation's busiest airports with closely spaced parallel runways for arrivals, capacity can be reduced significantly when weather at these airports falls below visual approach minima. When visual approaches can be used for arriving aircraft,

Laurence Audenaerd; D. Domino; S. Lang; C. Lunsford; A. P. Smith; J. Tittsworth

2009-01-01

114

Environmental Information for the U.S. Next Generation Air Transportation System (NextGen)  

NASA Astrophysics Data System (ADS)

It is estimated that weather is responsible for approximately 70% of all air traffic delays and cancellations in the United States. Annually, this produces an overall economic loss of nearly 40B. The FAA and NASA have determined that weather impacts and other environmental constraints on the U.S. National Airspace System (NAS) will increase to the point of system unsustainability unless the NAS is radically transformed. A Next Generation Air Transportation System (NextGen) is planned to accommodate the anticipated demand for increased system capacity and the super-density operations that this transformation will entail. The heart of the environmental information component that is being developed for NextGen will be a 4-dimensional data cube which will include a single authoritative source comprising probabilistic weather information for NextGen Air Traffic Management (ATM) systems. Aviation weather constraints and safety hazards typically comprise meso-scale, storm-scale and microscale observables that can significantly impact both terminal and enroute aviation operations. With these operational impacts in mind, functional and performance requirements for the NextGen weather system were established which require significant improvements in observation and forecasting capabilities. This will include satellite observations from geostationary and/or polar-orbiting hyperspectral sounders, multi-spectral imagers, lightning mappers, space weather monitors and other environmental observing systems. It will also require improved in situ and remotely sensed observations from ground-based and airborne systems. These observations will be used to better understand and to develop forecasting applications for convective weather, in-flight icing, turbulence, ceilings and visibility, volcanic ash, space weather and the environmental impacts of aviation. Cutting-edge collaborative research efforts and results from NASA, NOAA and the FAA which address these phenomena are summarized. In 2003, a Joint Planning and Development Office (JPDO) was established by public law to meet the significant challenges that NextGen presents. JPDO partners were chartered which include, but are not limited to, the Federal Aviation Administration (FAA), the National Oceanic and Atmospheric Administration (NOAA), the National Aeronautics and Space Administration (NASA), the Department of Defense (DOD) and broad elements of academia and the aviation industry. This paper provides the aviation meteorology community with useful insight on salient NextGen environmental information requirements that have been developed by the JPDO Weather Working Group's Environmental Information Team. These efforts will help to define observation and forecast systems needed to support NextGen and to develop the operational applications for NextGen aviation weather information. Another major goal of this paper is to inform the international weather community of our research progress and plans for NextGen, to foster research collaboration with our colleagues, and to exchange information to maximize success of NextGen, SESAR and related initiatives world-wide.

Murray, J.; Miner, C.; Pace, D.; Minnis, P.; Mecikalski, J.; Feltz, W.; Johnson, D.; Iskendarian, H.; Haynes, J.

2009-09-01

115

Echidnotaenia tachyglossi (Johnston) gen. et comb. nov. (Anoplocephalata: Linstowiidae) from the monotreme Tachyglossus aculeatus Shaw in Australia.  

PubMed

Echidnotaenia gen. nov. (Anoplocephalata: Linstowiidae) is proposed for Cittotaenia tachyglossi Johnston, 1913 from the monotreme Tachyglossus acuteatus Shaw, 1792. The new genus is distinguished from other genera of the Linstowiidae by its paired genitalia and aporally extended vitellaria. PMID:7410808

Beveridge, I

1980-06-01

116

Mercury: Next-gen Data Analysis and Annotation Pipeline (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)  

SciTech Connect

David Sexton (Baylor) gives a talk titled "Mercury: Next-gen Data Analysis and Annotation Pipeline" at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

Sexton, David (Baylor)

2012-06-01

117

Mercury: Next-gen Data Analysis and Annotation Pipeline (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)  

ScienceCinema

David Sexton (Baylor) gives a talk titled "Mercury: Next-gen Data Analysis and Annotation Pipeline" at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

118

Towards Structuring Unstructured GenBank Metadata for Enhancing Comparative Biological Studies  

PubMed Central

Within large sequence repositories such as GenBank there is a wealth of metadata providing contextual information that may enhance search and retrieval of relevant sequences for a range of subsequent analyses. One challenge is the use of free-text in these metadata fields where approaches are needed to extract, structure, and encode essential information. The goal of the present study was to explore the feasibility of using a combination of existing resources for annotating unstructured GenBank metadata, initially focusing on the “host” and “isolation_source” fields. This paper summarizes early results for 10 host organisms that include a characterization of associated isolation sources with respect to biomedical ontologies and semantic types. The findings from this preliminary study provide insights to the rich amount of information captured within these unstructured metadata, guidance for addressing the challenges and issues encountered, and highlight the potential value for enriching comparative biological studies towards improving human health.

Chen, Elizabeth S.; Sarkar, Indra Neil

2011-01-01

119

GenEvA (II): a phase space generator from a reweighted parton shower  

NASA Astrophysics Data System (ADS)

We introduce a new efficient algorithm for phase space generation. A parton shower is used to distribute events across all of multiplicity, flavor, and phase space, and these events can then be reweighted to any desired analytic distribution. To verify this method, we reproduce the e+e- ? n jets tree-level result of traditional matrix element tools. We also show how to improve tree-level matrix elements automatically with leading-logarithmic resummation. This algorithm is particularly useful in the context of a new framework for event generation called GenEvA. In a companion paper [1], we show how the GenEvA framework can address contemporary issues in event generation.

Bauer, Christian W.; Tackmann, Frank J.; Thaler, Jesse

2008-12-01

120

A REVIEW OF AGING EFFECTS IN ALLOY 617 FOR GEN IV NUCLEAR REACTOR APPLICATIONS  

SciTech Connect

The literature was reviewed of aging and aging effects in Alloy 617 to determine the supplementary data needed to understand the response of the alloy to long-time exposure conditions being considered for structural components in Gen IV nuclear reactors. Most of the data were produced in connection with the international research effort supporting High Temperature Gas-Cooled Reactor (HTGR) projects in the 1970s and 1980s. Topics considered included microstructural changes, hardness, tensile properties, toughness, creep-rupture, fatigue, and crack growth. It became clear that, for the long-time, very high temperature conditions of the Gen IV reactors, a significant effort would be needed to fully understand and characterize property changes. Several topics for further research were recommended.

Ren, Weiju [ORNL; Swindeman, Robert W [ORNL

2006-01-01

121

A REVIEW PAPER ON AGING EFFECTS IN ALLOY 617 FOR GEN IVNUCLEAR REACTOR APPLICATIONS  

SciTech Connect

To understand the response of Alloy 617 to long-time exposure conditions and determine the supplementary data needs for structural components in Gen IV nuclear reactors, the literature of aging and aging effects in the alloy was reviewed. Most of the reviewed data were produced in connection with the international research effort supporting High Temperature Gas-Cooled Reactor (HTGR) projects in the 1970s and 1980s. Topics considered included microstructural changes, hardness, tensile properties, toughness, creep-rupture, fatigue, and crack growth. It became clear that, for the long-time, very high temperature conditions of the Gen IV reactors, a significant effort would be needed to fully understand and characterize property changes. Several topics for further research were recommended.

Ren, Weiju [ORNL; Swindeman, Robert W [ORNL

2009-01-01

122

Dual-track CCS stakeholder engagement: Lessons learned from FutureGen in Illinois  

USGS Publications Warehouse

FutureGen, as originally planned, was to be the world's first coal-fueled, near-zero emissions power plant with fully integrated, 90% carbon capture and storage (CCS). From conception through siting and design, it enjoyed strong support from multiple stakeholder groups, which benefited the overall project. Understanding the stakeholder engagement process for this project provides valuable insights into the design of stakeholder programs for future CCS projects. FutureGen is one of few projects worldwide that used open competition for siting both the power plant and storage reservoir. Most site proposals were coordinated by State governments. It was unique in this and other respects relative to the site selection method used on other DOE-supported projects. At the time of site selection, FutureGen was the largest proposed facility designed to combine an integrated gasification combined cycle (IGCC) coal-fueled power plant with a CCS system. Stakeholder engagement by states and the industry consortium responsible for siting, designing, building, and operating the facility took place simultaneously and on parallel tracks. On one track were states spearheading state-wide site assessments to identify candidate sites that they wanted to propose for consideration. On the other track was a public-private partnership between an industry consortium of thirteen coal companies and electric utilities that comprised the FutureGen Alliance (Alliance) and the U.S. Department of Energy (DOE). The partnership was based on a cooperative agreement signed by both parties, which assigned the lead for siting to the Alliance. This paper describes the stakeholder engagement strategies used on both of these tracks and provides examples from the engagement process using the Illinois semi-finalist sites. ?? 2011 Published by Elsevier Ltd.

Hund, G.; Greenberg, S. E.

2011-01-01

123

Fracture of the polyethylene tibial post in a NexGen posterior-stabilized knee prosthesis  

Microsoft Academic Search

We reported a case of fracture of a polyethylene tibial post in a 44-year-old woman after 3 years of NexGen posterior-stabilized total knee arthroplasty (Zimmer, Warsaw, IN). Burnishing and delamination of the polyethylene was found around the breakage site of the post, especially over the anterior aspect of the post base. It indicated that the possible failure mechanism was the

Yen-Shuo Chiu; Wei-Ming Chen; Ching-Kuei Huang; Chao-Ching Chiang; Tain-Hsiung Chen

2004-01-01

124

NAS-wide simulation and passenger itinerary performance: Implications for NextGen benefits analysis  

Microsoft Academic Search

NAS-wide simulations are one of the methods used to estimate annual system-wide benefits for Air Traffic Control modernization concepts-of-operations and technologies (e.g. NextGen\\/SESAR). These tools simulate the operation of up to 60,000 flights per day in various combinations of demand (i.e. flights) and capacity (i.e. airport and airspace capacity). The main input to the simulation is a schedule of flights

Lance Sherry

2011-01-01

125

ShieldGen: Automatic Data Patch Generation for Unknown Vulnerabilities with Informed Probing  

Microsoft Academic Search

In this paper, we present ShieldGen, a system for au- tomatically generating a data patch or a vulnerability signature for an unknown vulnerability, given a zero-day attack instance. The key novelty in our work is that we leverage knowledge of the data format to generate new potential attack instances, which we call probes, and use a zero-day detector as an

Weidong Cui; Marcus Peinado; Helen J. Wang; Michael E. Locasto

2007-01-01

126

MicroGen: a MIAME compliant web system for microarray experiment information and workflow management  

PubMed Central

Background Improvements of bio-nano-technologies and biomolecular techniques have led to increasing production of high-throughput experimental data. Spotted cDNA microarray is one of the most diffuse technologies, used in single research laboratories and in biotechnology service facilities. Although they are routinely performed, spotted microarray experiments are complex procedures entailing several experimental steps and actors with different technical skills and roles. During an experiment, involved actors, who can also be located in a distance, need to access and share specific experiment information according to their roles. Furthermore, complete information describing all experimental steps must be orderly collected to allow subsequent correct interpretation of experimental results. Results We developed MicroGen, a web system for managing information and workflow in the production pipeline of spotted microarray experiments. It is constituted of a core multi-database system able to store all data completely characterizing different spotted microarray experiments according to the Minimum Information About Microarray Experiments (MIAME) standard, and of an intuitive and user-friendly web interface able to support the collaborative work required among multidisciplinary actors and roles involved in spotted microarray experiment production. MicroGen supports six types of user roles: the researcher who designs and requests the experiment, the spotting operator, the hybridisation operator, the image processing operator, the system administrator, and the generic public user who can access the unrestricted part of the system to get information about MicroGen services. Conclusion MicroGen represents a MIAME compliant information system that enables managing workflow and supporting collaborative work in spotted microarray experiment production.

Burgarella, Sarah; Cattaneo, Dario; Pinciroli, Francesco; Masseroli, Marco

2005-01-01

127

Development of an Enhanced GenVARR™ (Generator Volt Ampere Reactive Reserve) System  

SciTech Connect

Transmission system operators require near real time knowledge of reactive power capability to reliably operate large electric power transmission systems. Reactive power produced by, or capable of being produced by, a power generator is often estimated based on a series of mega volt amperes (MVA) capability curves for the generator. These curves indicate the ability of the generator to produce real and reactive power under a variety of conditions. In transmission planning and operating studies, it is often assumed, based on estimates for these capability curves, that the generator can provide its rated MVA capability output when needed for system stability However, generators may not always operate at levels depicted by the maximum MVA capability curve due to present constraints. Transmission system operators utilizing the generators’ capability curves for operation decisions regarding transmission system stability or for planning horizons may overestimate the capability of the generators to supply reactive power when required. Southern Company has enhanced GenVARR(TM), the system of plant data query, retrieval, and analysis and calculates the actual – not estimated -- remaining reactive power output capability. The remaining reactive output is considered spinning reserve and is displayed graphically to transmission control center and generating plant operators to identify real time VAR limits. GenVARR is capable of aggregating generators from a defined region, or other user selectable combinations, to represent the available reserves that the operators are specifically interested in. GenVARR(TM) has been put into live production operation and is expected to significantly improve the overall visibility of the reactive reserve capability of the system. This new version of GenVARR(TM) significantly enhances the products structure and performance, and enables links to other key transmission system operation tools.

Schatz, Joe E.

2009-03-12

128

Reclassification of Cellulomonas cellulans (Stackebrandt and Keddie 1986) as Cellulosimicrobium cellulans gen. nov., comb. nov.  

PubMed

Phylogenetic analysis of 16S rDNA provides evidence that Cellulomonas cellulans branches outside the phylogenetic confines of the genus Cellulomonas. The distinct phylogenetic and chemotaxonomic status of Cellulomonas cellulans as a phylogenetic neighbour of the genus Promicromonospora, justifies the description of a new genus for which the name Cellulosimicrobium gen. nov. with the type species Cellulosimicrobium cellulans comb. nov. is proposed. PMID:11411667

Schumann, P; Weiss, N; Stackebrandt, E

2001-05-01

129

Dobbertiniopteryx capniomimus gen. et sp. nov. die erste Steinfliege (Insecta: Plecoptera) aus dem europäischen Jura  

Microsoft Academic Search

\\u000a Abstract  From the Upper Liassic of Dobbertin (Mecklenburg, Germany) the first stoneflyDobbertiniopteryx capniomimus gen. et sp. nov. is described. It is probably a representative of the Capniidae (Plecoptera: Nemouroidea) or of its stemgroup.\\u000a Slowly running fresh water streams and stagnant water bodies in coastal regions are considered an ecological cause of the\\u000a rarity of Plecoptera in European Jurassic sediments.

Jörg Ansorge

1993-01-01

130

Genes and proteins of Escherichia coli K-12 (GenProtEC)  

Microsoft Academic Search

GenProtEC is a database of Escherichia coli genes and their gene products, classified by type of function and physiological role and with citations to the literature for each. Also p resent a re d ata on sequence s imilarities among E.coli proteins, r epresenting g roups o f p ara- logous genes, w ith P AM v alues, p ercent

Monica Riley

1997-01-01

131

Bias explorer: measurements of compositional bias in EMBL and GenBank sequence files  

Microsoft Academic Search

A Windows application for compositional analysis of sequenced genomes (EMBL or GenBank flat files) is available as freeware.\\u000a The application allows the user to quantify word bias using Markov chain analysis and it allows the user to generate sliding\\u000a window data for GC-skew, AT-skew, purine excess, keto excess and discrete word counts. The mathematical routines reside in\\u000a a dynamic link

Anders Fuglsang

2004-01-01

132

Structural materials for Gen-IV nuclear reactors: Challenges and opportunities  

Microsoft Academic Search

Generation-IV reactor design concepts envisioned thus far cater toward a common goal of providing safer, longer lasting, proliferation-resistant and economically viable nuclear power plants. The foremost consideration in the successful development and deployment of Gen-IV reactor systems is the performance and reliability issues involving structural materials for both in-core and out-of-core applications. The structural materials need to endure much higher

K. L. Murty; I. Charit

2008-01-01

133

ConfGen: a conformational search method for efficient generation of bioactive conformers.  

PubMed

We describe the methodology, parametrization, and application of a conformational search method, called ConfGen, designed to efficiently generate bioactive conformers. We define efficiency as the ability to generate a bioactive conformation within a small total number of conformations using a reasonable amount of computer time. The method combines physics-based force field calculations with empirically derived heuristics designed to achieve efficient searching and prioritization of the ligand's conformational space. While many parameter settings are supported, four modes spanning a range of speed and quality trades-offs are defined and characterized. The validation set used to test the method is composed of ligands from 667 crystal structures covering a broad array of target and ligand classes. With the fastest mode, ConfGen uses an average of 0.5 s per ligand and generates only 14.3 conformers per ligand, at least one of which lies within 2.0 A root-mean-squared deviation of the crystal structure for 96% of the ligands. The most computationally intensive mode raises this recovery rate to 99%, while taking 8 s per ligand. Combining multiple search modes to "fill-in" holes in the conformation space or energy minimizing using an all-atom force field each lead to improvements in the recovery rates at higher resolutions. Overall, ConfGen is at least as good as competing programs at high resolution and demonstrates higher efficiency at resolutions sufficient for many downstream applications, such as pharmacophore modeling. PMID:20373803

Watts, K Shawn; Dalal, Pranav; Murphy, Robert B; Sherman, Woody; Friesner, Rich A; Shelley, John C

2010-04-26

134

GenColors-based comparative genome databases for small eukaryotic genomes  

PubMed Central

Many sequence data repositories can give a quick and easily accessible overview on genomes and their annotations. Less widespread is the possibility to compare related genomes with each other in a common database environment. We have previously described the GenColors database system (http://gencolors.fli-leibniz.de) and its applications to a number of bacterial genomes such as Borrelia, Legionella, Leptospira and Treponema. This system has an emphasis on genome comparison. It combines data from related genomes and provides the user with an extensive set of visualization and analysis tools. Eukaryote genomes are normally larger than prokaryote genomes and thus pose additional challenges for such a system. We have, therefore, adapted GenColors to also handle larger datasets of small eukaryotic genomes and to display eukaryotic gene structures. Further recent developments include whole genome views, genome list options and, for bacterial genome browsers, the display of horizontal gene transfer predictions. Two new GenColors-based databases for two fungal species (http://fgb.fli-leibniz.de) and for four social amoebas (http://sacgb.fli-leibniz.de) were set up. Both new resources open up a single entry point for related genomes for the amoebozoa and fungal research communities and other interested users. Comparative genomics approaches are greatly facilitated by these resources.

Felder, Marius; Romualdi, Alessandro; Petzold, Andreas; Platzer, Matthias; Suhnel, Jurgen; Glockner, Gernot

2013-01-01

135

GenColors-based comparative genome databases for small eukaryotic genomes.  

PubMed

Many sequence data repositories can give a quick and easily accessible overview on genomes and their annotations. Less widespread is the possibility to compare related genomes with each other in a common database environment. We have previously described the GenColors database system (http://gencolors.fli-leibniz.de) and its applications to a number of bacterial genomes such as Borrelia, Legionella, Leptospira and Treponema. This system has an emphasis on genome comparison. It combines data from related genomes and provides the user with an extensive set of visualization and analysis tools. Eukaryote genomes are normally larger than prokaryote genomes and thus pose additional challenges for such a system. We have, therefore, adapted GenColors to also handle larger datasets of small eukaryotic genomes and to display eukaryotic gene structures. Further recent developments include whole genome views, genome list options and, for bacterial genome browsers, the display of horizontal gene transfer predictions. Two new GenColors-based databases for two fungal species (http://fgb.fli-leibniz.de) and for four social amoebas (http://sacgb.fli-leibniz.de) were set up. Both new resources open up a single entry point for related genomes for the amoebozoa and fungal research communities and other interested users. Comparative genomics approaches are greatly facilitated by these resources. PMID:23193285

Felder, Marius; Romualdi, Alessandro; Petzold, Andreas; Platzer, Matthias; Sühnel, Jürgen; Glöckner, Gernot

2012-11-28

136

Ultrastructure and molecular phylogeny of two heterolobosean amoebae, Euplaesiobystra hypersalinica gen. et sp. nov. and Tulamoeba peronaphora gen. et sp. nov., isolated from an extremely hypersaline habitat.  

PubMed

We isolated two amoebae, Tulamoeba peronaphora gen. et sp. nov. and Euplaesiobystra hypersalinica gen. et sp. nov. from the high salinity waters (293-300 per thousand salinity) of a Korean solar saltern. These new species show features typical of Heterolobosea - a limax form with eruptive pseudopodial formation, flattened/discoidal mitochondrial cristae, cysts with plugged pores, and no discrete, stacked dictyosomes. 18S rRNA gene phylogenies place both species within the Heterolobosea. Tulamoeba peronaphora appears to lack a flagellate phase, and has one cyst pore that penetrates the cyst wall. In 18S rRNA gene trees, Tulamoeba peronaphora is specifically related to Pleurostomum flabellatum, an extreme halophile that is observed only as a flagellate. Its next closest relatives are Naegleria and Willaertia. Euplaesiobystra hypersalinica has 2-4 cyst pores in the ectocyst wall (only), and has a bi-flagellated flagellate phase with no obvious cytostome. Its closest described relative is Heteramoeba clara, which is marine, has a cytostome, lacks cyst pores, and has a different nucleolus organization. The Euplaesiobystra hypersalinica 18S rRNA gene is 99.5% identical to a sequence accessed under the nomen nudum 'Plaesiobystra hypersalinica' - we consider them the same species. Tulamoeba peronaphora grows at 75-250 per thousand salinity, while E. hypersalinica grows at 100-300 per thousand (at least) salinity. Both amoebae seem to be 'extreme halophiles', and their ancestors invaded high salinity environments independently of each other. These results provide more evidence that there is a substantial ecological and phylogenetic diversity of heterotrophic eukaryotes capable of growing in very high salinity environments, and these ecosystems may be more complex than usually assumed. PMID:19121603

Park, Jong Soo; Simpson, Alastair G B; Brown, Susan; Cho, Byung Cheol

2009-01-01

137

iGen 0.1: the automated generation of a parameterisation of entrainment in marine stratocumulus  

NASA Astrophysics Data System (ADS)

In a previous paper we described a new technique for automatically generating parameterisations using a program called iGen. iGen generates parameterisations by analysing the source code of a~high resolution model that resolves the physics to be parameterised. In order to demonstrate that this technique scales up to deal with models of realistic complexity we have used iGen to generate a parameterisation of entrainment in marine stratocumulus. We describe how iGen was used to analyse the source code of an eddy resolving model (ERM) and generate a parameterisation of entrainment velocity in marine stratocumulus in terms of the large-scale state of the boundary layer. The parameterisation was tested against results from the DYCOMS-II intercomparison of ERM models and iGen's parameterisation of mean entrainment velocity was found to be 5.27 × 10-3 ± 0.62 × 10-3 m s-1 compared to 5.2 × 10-3 ± 0.8 × 10-3 m s-1 for the DYCOMS-II ensemble of large eddy simulation (LES) models.

Tang, D. F.; Dobbie, S.

2011-09-01

138

Technology discussion of reducing the equivalent background illumination of Gen ? Image Intensifier  

NASA Astrophysics Data System (ADS)

As the development of Gen III Image Intensifier, photocathode sensitivity, spatial static resolution and signal-to-noise ratio of the devices are continuously improved except for the view effect. However, for most devices, the equivalent background illumination (EBI) is excessive, and considerable part is more than an order of magnitude. Many factors have an effect on the EBI of the Gen III Image Intensifier. By academic analysis and experiment research, it is demonstrated that: It is the thermal electron emission of photocathode, dark current, gain of micro-channel plate (MCP) with ion barrier film(IBF), electric field strength between MCP and photocathode and the light feedback of phosphor that lend to the EBI, but for the phosphor screen made by the normal process, because of the aluminum film, EBI caused by the optical feedback is slightly lower, which can not cause the excessive EBI. For the MCP with IBF after normal processing, even the first focused voltage is added to 350V, the EBI does not exceed the highest value of 1.66×10-7 allowed by national military standard. Needless to say the photocathode is the focus factor of the EBI after excluding the phosphor screen, the MCP and other influencing factors. It is believed that the thermal electron emission of photocathode leads to the excessive EBI. Finally, without reducing the photocathode sensitivity, by optimizing activation technics, i.e., reduce CsO quantity, and aging test disposal, the thermal electron emission is weaken, the EBI is becoming lower, most of the products satisfy with request of technical standard in this index. That is valuable to accelerate the engineering of Gen III Image Intensifier.

Zhu, Yu-feng; Zhang, Ni; Li, Dan; Nie, Jing; Zhang, Tai-min; Liu, Xiao-jian; Liu, Zhao-lu; Fu, Ling-Yun

2013-08-01

139

Evaluation of Gen-Probe's Histoplasma capsulatum and Cryptococcus neoformans AccuProbes.  

PubMed Central

Gen-Probe's DNA probes were evaluated for use in the identification of clinical isolates of Histoplasma capsulatum var. capsulatum and Cryptococcus neoformans. Ninety-five mould-phase fungi were probed, including 41 isolates of H. capsulatum var. capsulatum. Similarly, 98 yeasts, including 42 C. neoformans isolates, were examined by using the C. neoformans DNA probe. In the study, both probes demonstrated 100% specificity and 100% sensitivity. Their use in the clinical laboratory may significantly reduce the time required for definitive identification of fungi.

Huffnagle, K E; Gander, R M

1993-01-01

140

Gen IV Materials Handbook Functionalities and Operation (2B) Handbook Version 2.0  

SciTech Connect

This document is prepared for navigation and operation of the Gen IV Materials Handbook, with architecture description and new user access initiation instructions. Development rationale and history of the Handbook is summarized. The major development aspects, architecture, and design principles of the Handbook are briefly introduced to provide an overview of its past evolution and future prospects. Detailed instructions are given with examples for navigating the constructed Handbook components and using the main functionalities. Procedures are provided in a step-by-step fashion for Data Upload Managers to upload reports and data files, as well as for new users to initiate Handbook access.

Ren, Weiju [ORNL

2011-08-01

141

Pilum pilum gen. et sp. n. (Acanthocephala: Echinorhynchidae) from freshwater fishes of the southeastern United States.  

PubMed

Pilum pilum gen. et sp. n. is described from the warmouth, Lepomis gulosus (Cuvier); brown bullhead, Ictalurus nebulosus (Lesueur); yellow bullhead, I. natalis (Lesueur); redbreast sunfish, L. auritus (Linnaeus); bluegill, L. macrochirus Rafinesque; spotted sunfish, L. punctatus (Valenciennes); and redfin pickerel, Esox americanus (Gmelin), from the Alabama River Drainage, brown bullhead from the Mobile Bay Drainage in Alabama, and pirate perch, Aphredoderus sayanus Gilliams, from an Atlantic Coast drainage in Georgia. The new genus most closely resembles the genus Acanthocephalus; it differs from this genus in having a distinctive pear-shaped proboscis, a long neck, and hooks which abruptly differ in size. PMID:1255353

Williams, E H

1976-02-01

142

Kennedy Space Center Next Gen Site: Routine, Affordable Access to Space  

NSDL National Science Digital Library

The Next Gen Site, operated by the National Aeronautics and Space Administration at Kennedy Space Center, is investigating ways of making space travel more routine and affordable. The site offers many reports on the Vision Spaceport Partnership, the Highly Reusable Space Transportation Project, Space Solar Power, and Space Transportation System Affordability. A map of Cape Canaveral highlights each launch pad, and you can see information on each one by clicking on it. Related Info Including X-Vehicles is a section with background on several experimental projects and has links to sites that examine different aspects of design and planning for easier access to space.

1997-01-01

143

POWER-GEN `96 international. Book I - A. Electric power trends & strategies, Volume 1-3  

SciTech Connect

This is the first book in a six book set for the Power-Gen 96 International Conference and Exhibition. This book contains Volumes 1 through 3. Topics covered by volumes 1 through 3 include: global power industry trends, North American power industry trends, and fuels. Subtopics include: emerging markets, project financing and risk management, project development case studies, key issues in re-structuring, competitive strategies, power marketing infrastructure development, global fuel resources, opportunity and emerging fuels, fuel quality and safety, and privatization and politics of power.

NONE

1996-12-31

144

Bias explorer: measurements of compositional bias in EMBL and GenBank sequence files.  

PubMed

A Windows application for compositional analysis of sequenced genomes (EMBL or GenBank flat files) is available as freeware. The application allows the user to quantify word bias using Markov chain analysis and it allows the user to generate sliding window data for GC-skew, AT-skew, purine excess, keto excess and discrete word counts. The mathematical routines reside in a dynamic link library (DLL), which can be used independently by other applications. The software is available for download at http://www.dfuni.dk/~anfu/Bioinformatics/Main.htm. PMID:15702383

Fuglsang, Anders

2004-11-01

145

Considerations of Alloy 617 Application in the Gen IV Nuclear Reactor Systems - Part I: Mechanical Property Challenges  

SciTech Connect

Alloy 617 is currently considered as a leading candidate material for high temperature components in the Gen IV Nuclear Reactor Systems. Because of the unprecedented severe working conditions beyond its commercial service experience required by the Gen IV systems, the alloy faces various challenges in both mechanical and metallurgical properties. This paper, as Part I of the discussion, is focused on the challenges and issues in the mechanical properties of Alloy 617 for the intended nuclear application. Considerations are given in details in its mechanical property data scatter, low creep strength in the desired high temperature range, lack of longterm creep curves, high loading rate dependency, and preponderant tertiary creep. Some research and development activities are suggested with discussions on their viability to satisfy the Gen IV Nuclear Reactor System needs in near future and in the long run.

Ren, Weiju [ORNL

2010-01-01

146

Aircraft deconfliction responsibility across en-route sectors in NextGen separation assurance  

NASA Astrophysics Data System (ADS)

The subject of the current research is a Next Generation Air Transportation System (NextGen) concept that involves automated separation assurance developed to enable controllers to provide both safe and efficient air traffic services at much higher traffic densities than possible today. The study investigated the issue of how responsibility should be handled between controllers for the resolution of a conflict that is predicted to occur in a sector other than where it was detected. Two possibilities, a De-Conflicting AirPlanes procedure (DCAP) versus a De-Conflicting AirSpace procedure (DCAS), were examined under human-in-the-loop simulations with scripted aircraft conflicts. Results showed that the DCAS procedure was preferred and that participants experienced less verbal coordination and took less time to resolve conflicts. The results, however, did not reveal significant differences among other plane performance metrics between DCAP and DCAS. These results indicate that the demands of NextGen separation assurance might still be met with ownership and coordination procedures (e.g., DCAP) similar to today. Reducing verbal coordination requirements, however, and allowing separation assurance responsibilities to extend more seamlessly across sector boundaries (e.g., DCAS) would evidently be more acceptable to controllers.

Cabrall, Christopher D.

147

GenNon-h: Generating multiple sequence alignments on nonhomogeneous phylogenetic trees  

PubMed Central

Background A number of software packages are available to generate DNA multiple sequence alignments (MSAs) evolved under continuous-time Markov processes on phylogenetic trees. On the other hand, methods of simulating the DNA MSA directly from the transition matrices do not exist. Moreover, existing software restricts to the time-reversible models and it is not optimized to generate nonhomogeneous data (i.e. placing distinct substitution rates at different lineages). Results We present the first package designed to generate MSAs evolving under discrete-time Markov processes on phylogenetic trees, directly from probability substitution matrices. Based on the input model and a phylogenetic tree in the Newick format (with branch lengths measured as the expected number of substitutions per site), the algorithm produces DNA alignments of desired length. GenNon-h is publicly available for download. Conclusion The software presented here is an efficient tool to generate DNA MSAs on a given phylogenetic tree. GenNon-h provides the user with the nonstationary or nonhomogeneous phylogenetic data that is well suited for testing complex biological hypotheses, exploring the limits of the reconstruction algorithms and their robustness to such models.

2012-01-01

148

Distribution of Hammerhead and Hammerhead-like RNA Motifs Through the GenBank  

PubMed Central

Hammerhead ribozymes previously were found in satellite RNAs from plant viroids and in repetitive DNA from certain species of newts and schistosomes. To determine if this catalytic RNA motif has a wider distribution, we decided to scrutinize the GenBank database for RNAs that contain hammerhead or hammerhead-like motifs. The search shows a widespread distribution of this kind of RNA motif in different sequences suggesting that they might have a more general role in RNA biology. The frequency of the hammerhead motif is half of that expected from a random distribution, but this fact comes from the low CpG representation in vertebrate sequences and the bias of the GenBank for those sequences. Intriguing motifs include those found in several families of repetitive sequences, in the satellite RNA from the carrot red leaf luteovirus, in plant viruses like the spinach latent virus and the elm mottle virus, in animal viruses like the hepatitis E virus and the caprine encephalitis virus, and in mRNAs such as those coding for cytochrome P450 oxidoreductase in the rat and the hamster.

Ferbeyre, Gerardo; Bourdeau, Veronique; Pageau, Marie; Miramontes, Pedro; Cedergren, Robert

2000-01-01

149

Gen-2 hand-held optical imager towards cancer imaging: reflectance and transillumination phantom studies.  

PubMed

Hand-held near-infrared (NIR) optical imagers are developed by various researchers towards non-invasive clinical breast imaging. Unlike these existing imagers that can perform only reflectance imaging, a generation-2 (Gen-2) hand-held optical imager has been recently developed to perform both reflectance and transillumination imaging. The unique forked design of the hand-held probe head(s) allows for reflectance imaging (as in ultrasound) and transillumination or compressed imaging (as in X-ray mammography). Phantom studies were performed to demonstrate two-dimensional (2D) target detection via reflectance and transillumination imaging at various target depths (1-5 cm deep) and using simultaneous multiple point illumination approach. It was observed that 0.45 cc targets were detected up to 5 cm deep during transillumination, but limited to 2.5 cm deep during reflectance imaging. Additionally, implementing appropriate data post-processing techniques along with a polynomial fitting approach, to plot 2D surface contours of the detected signal, yields distinct target detectability and localization. The ability of the gen-2 imager to perform both reflectance and transillumination imaging allows its direct comparison to ultrasound and X-ray mammography results, respectively, in future clinical breast imaging studies. PMID:22438743

Gonzalez, Jean; Roman, Manuela; Hall, Michael; Godavarty, Anuradha

2012-02-10

150

Characterization of autosomal copy-number variation in African Americans: the HyperGEN Study  

PubMed Central

African Americans are a genetically diverse population with a high burden of many, common heritable diseases. However, our understanding of genetic variation in African Americans is substandard because of a lack of published population-based genetic studies. We report the distribution of copy-number variation (CNV) in African Americans collected as part of the Hypertension Genetic Epidemiology Network (HyperGEN) using the Affymetrix 6.0 array and the CNV calling algorithms Birdsuite and PennCNV. We present population estimates of CNV from 446 unrelated African-American subjects randomly selected from the 451 families collected within HyperGEN. Although the majority of CNVs discovered were individually rare, we found the frequency of CNVs to be collectively high. We identified a total of 11?070 CNVs greater than 10?kb passing quality control criteria that were called by both algorithms – leading to an average of 24.8 CNVs per person covering 2214?kb (median). We identified 1541 unique copy-number variable regions, 309 of which did not overlap with the Database of Genomic Variants. These results provide further insight into the distribution of CNV in African Americans.

Wineinger, Nathan E; Pajewski, Nicholas M; Kennedy, Richard E; Wojczynski, Mary K; Vaughan, Laura K; Hunt, Steven C; Gu, C Charles; Rao, Dabeeru C; Lorier, Rachel; Broeckel, Ulrich; Arnett, Donna K; Tiwari, Hemant K

2011-01-01

151

Advanced Technology Development Program for Lithium-Ion Batteries: Gen 2 GDR Performance Evaluation Report  

SciTech Connect

The Advanced Technology Development Program has completed the performance evaluation of the second generation of lithium-ion cells (i.e., Gen 2 cells). This report documents the testing and analysis of the Gen 2 GDR cells, which were used to learn and debug the newly developed Technology Life Verification Test Manual. The purpose of the manual is to project a 15-year, 150,000 mile battery life capability with a 90% confidence interval using predictive models and short-term testing. The GDR cells were divided into two different matrices. The core-life test matrix consisted of calendar- and cycle-life cells with various changes to the four major acceleration factors (temperature, state-of-charge, throughput, and power rating). The supplemental-life test matrix consisted of cells subjected either to a path dependence study, or a comparison between the standard hybrid pulse power characterization test and the newly-developed minimum pulse power characterization test. Resistance and capacity results are reported.

Jon P. Christophersen; Chinh D. Ho; Gary L. Henriksen; David Howell

2006-07-01

152

Bellilinea caldifistulae gen. nov., sp. nov. and Longilinea arvoryzae gen. nov., sp. nov., strictly anaerobic, filamentous bacteria of the phylum Chloroflexi isolated from methanogenic propionate-degrading consortia.  

PubMed

Thermophilic (strain GOMI-1(T)) and mesophilic (strain KOME-1(T)) strains were isolated from two different cultures of propionate-degrading consortia obtained from thermophilic digester sludge and rice paddy soil, respectively. The two strains were non-spore-forming, non-motile and Gram-negative. Both strains were obligately anaerobic micro-organisms, showing multicellular filamentous morphotypes more than 100 mum in length. The cell width for strain GOMI-1(T) was 0.2-0.4 mum and that of strain KOME-1(T) was 0.4-0.6 mum. Strain GOMI-1(T) could grow at 45-65 degrees C with a pH range of 6.0-7.5 (optimum growth at 55 degrees C, pH 7.0). The temperature range for growth of strain KOME-1(T) was 30-40 degrees C and the pH range was pH 5.0-8.5 (optimum growth around 37 degrees C, pH 7.0). Yeast extract was required for growth of both strains. Strain GOMI-1(T) was able to grow with a number of carbohydrates in the presence of yeast extract. In yeast extract-containing medium, strain KOME-1(T) could utilize proteins and a limited range of sugars for growth. The G+C contents of the DNA of strains GOMI-1(T) and KOME-1(T) were respectively 54.7 and 57.6 mol%. Major fatty acids of strain GOMI-1(T) were C(16 : 0), C(14 : 0) and iso-C(15 : 0), whereas those of strain KOME-1(T) were iso-C(15 : 0), anteiso-C(15 : 0) and C(14 : 0). Based on comparative analysis of 16S rRNA gene sequences of strains GOMI-1(T) and KOME-1(T), the strains were placed in different phylogenetic positions in the class Anaerolineae of the bacterial phylum Chloroflexi. Their phenotypic and genetic traits strongly supported the conclusion that the strains should be described as two independent taxa in the class Anaerolineae. Hence, we propose the names Bellilinea caldifistulae gen. nov., sp. nov., and Longilinea arvoryzae gen. nov., sp. nov., for strains GOMI-1(T) and KOME-1(T). The type strains of Bellilinea caldifistulae and Longilinea arvoryzae are respectively GOMI-1(T) (=JCM 13669(T) =DSM 17877(T)) and KOME-1(T) (=JCM 13670(T) =KTCC 5380(T)). PMID:17911301

Yamada, Takeshi; Imachi, Hiroyuki; Ohashi, Akiyoshi; Harada, Hideki; Hanada, Satoshi; Kamagata, Yoichi; Sekiguchi, Yuji

2007-10-01

153

A REVIEW ON CURRENT STATUS OF ALLOYS 617 AND 230 FOR GEN IV NUCLEAR REACTOR INTERNALS AND HEAT EXCHANGERS  

SciTech Connect

Alloys 617 and 230 are currently identified as two leading candidate metallic materials in the down selection for applications at temperatures above 760 C in the Gen IV Nuclear Reactor Systems. Qualifying the materials requires significant information related to Codification, mechanical behavior modeling, metallurgical stability, environmental resistance, and many other aspects. In the present paper, material requirements for the Gen IV Nuclear Reactor Systems are discussed; certain available information regarding the two alloys under consideration for the intended applications are reviewed and analyzed. Suggestions are presented for further R&D activities for the materials selection.

Ren, Weiju [ORNL; Swindeman, Robert W [ORNL

2009-01-01

154

Rationale and Design of the National Registry of Genetically Triggered Thoracic Aortic Aneurysms and Cardiovascular Conditions (GenTAC) Registry  

PubMed Central

Background Although the management of thoracic aortic aneurysms (TAAs) has improved significantly, patients presenting with aortic dissections, rupture or other acute complications of TAAs continue to suffer high rates of morbidity and mortality. Accumulating data have indicated that many TAAs are due to underlying gene mutations. A comprehensive approach to the study of TAAs resulting from genetic mutations is needed to translate this information into advances in treatment. Objective The National Registry of Genetically Triggered Thoracic Aortic Aneurysms and Cardiovascular Conditions (GenTAC) was established to provide a biospecimen inventory and bioinformatics infrastructure to enable research to advance the clinical management of genetically-triggered TAAs and related complications. Methods The GenTAC Registry is a longitudinal observational cohort study enrolling patients with conditions related to genetically-induced TAAs from five regional clinical centers in the United States. Results Over 700 subjects with associated clinical histories, physical examinations, imaging data, and biospecimens have been enrolled in the Registry to date. Enrollment is expected to continue until September 2010. Total enrollment of nearly 3,000 subjects is expected. No interim analysis has yet been undertaken. Conclusions GenTAC has been established to facilitate studies by GenTAC investigators and others that will advance multiple scientific frontiers in thoracic aortic disease. Genotypic, proteomic, clinical, and imaging data will be integrated systematically with outcomes data to determine the optimal clinical management of patients suffering from genetically-induced TAAs.

2010-01-01

155

Transfer of Rhizobium loti, Rhizobium huakuii, Rhizobium mediterraneum, and Rhizobium to Mesorhizobium gen. nov. Rhizobium ciceri, tianshanense  

Microsoft Academic Search

Reasons are advanced for removal of Rhizobium ciceri, Rhizobium huakuii, Rhizobium loti, Rhizobium medi- terraneum, and Rhizobium tianshanense from the genus Rhizobium and for establishment of Mesorhizobium gen. nov. for these species. A description of the genus Mesorhizobium and amended descriptions of Mesorhizobium ciceri, Mesorhizobium huakuii, Mesorhizobium loti, Mesorhizobium mediterraneum, and Mezorhizobium tian- shanense are provided. In a review of

B. D. W. JARVIS; P. VAN BERKUM; W. X. CHEN; S. M. NOUR; M. P. FERNANDEZ; J. C. CLEYET-MAREL; M. GILLIS

156

Nuralagus rex, gen. et sp. nov., an endemic insular giant rabbit from the Neogene of Minorca (Balearic Islands, Spain)  

Microsoft Academic Search

We describe a new insular endemic lagomorph from the Late Neogene karstic deposits of Minorca (Balearic islands, Spain). Nuralagus rex, gen. et sp. nov., is characterized by an array of odd traits unknown for lagomorphs. Most outstanding are the gigantic size (average 12 kg), the robust postcranial skeleton with unique morphological traits (short manus and pes with splayed phalanges, short and

Josep Quintana; Meike Köhler; Salvador Moyà-Solà

2011-01-01

157

Paleoculicis minututs (Diptera: Culicidae) n. Gen., n. Sp., from Cretaceous Canadian amber, with a summary of described fossil mosquitoes  

Microsoft Academic Search

A new genus and species of fossil mosquito (Diptera: Culicidae) is described from Canadian Cretaceous amber, thus providing the first undeniable record of this group from the Cretaceous Period. Paleoculicis minutus n.gen., n.sp. can be separated from extant culicids by features of the head, thorax, and abdomen. Paleoculicis has closer affinities to the Culicinae than to the Anophelinae or Toxorhynchitinae.

George O. Poinar; T. J. Zavortinik; T. Pike; P. A. Johnston

2000-01-01

158

Palaeoleptus burmanicus n. gen., n. sp., an Early Cretaceous shore bug (Hemiptera: Palaeoleptidae n. fam.) in Burmese amber  

Microsoft Academic Search

Palaeoleptus burmanicus gen. et sp. nov. (Hemiptera: Leptopodomorpha: Palaeoleptidae fam. nov.) is described from Early Cretaceous Burmese amber. The fossil is characterized by nearly completely coreaceous wings with only a small membranous area at the distal tip, and a unique wing venation consisting of eight closed cells, including four obliquely orientated toward the embolar wing margin and two large vertically-positioned

George Poinar Jr.; Ron Buckley

2009-01-01

159

Gen Green: Changes in Australian Apprentices' and Trainees' Experience of Skills and Sustainability from 2008 to 2011  

ERIC Educational Resources Information Center

|The Gen Green research in 2008 and 2011 indicates that skills for sustainability public policy and business initiatives are having an impact, but that young skilled Australians' high level of interest in sustainability skills is confounded by a lack of guidance and incentives from employers, the market and educators. The research indicates that,…

Sack, Fabian

2012-01-01

160

Description of the terrestrial isopod mirtana costaricensis gen. et sp. n. from central America (Crustacea: Isopoda: Oniscidea)  

Microsoft Academic Search

An examination of isopod material deposited in the Museum of the University of Costa Rica, San Pedro, revealed a new genus and species of terrestrial isopods, Mirtana costaricensis gen. et sp. n. which is distinguished by its three?articulate antennal flagellum, incurved coxal plates and prominent neopleurae, while noduli laterales and respiratory areas on any pleopod are apparently lacking. Despite this

Andreas Leistikow

1997-01-01

161

Bottom-up synthesis of Zn1.7GeN1.8O nanoparticles for photocatalytic application  

NASA Astrophysics Data System (ADS)

Via a simple bottom-up approach, a complex quaternary oxynitride system (Zn1.7GeN1.8O) was prepared in the form of small nanoparticles (d ~ 15 nm), which were stable and morphologically well-defined. The Zn1.7GeN1.8O nanoparticles exhibited a band gap of 2.4 eV and were active towards photocatalytic degradation of organic dyes.Via a simple bottom-up approach, a complex quaternary oxynitride system (Zn1.7GeN1.8O) was prepared in the form of small nanoparticles (d ~ 15 nm), which were stable and morphologically well-defined. The Zn1.7GeN1.8O nanoparticles exhibited a band gap of 2.4 eV and were active towards photocatalytic degradation of organic dyes. Electronic supplementary information (ESI) available: SEM of the particles; absorption spectra; BET plot; TEM and XRD of the particles of the up-scaled synthesis; TEM of particles synthesized in the absence of ammonium chloride; IR-spectra; TGA plot; TEM of particles synthesized at 600 °C elemental analysis. See DOI: 10.1039/c3nr33561e

Schliehe, Constanze; Giordano, Cristina

2013-03-01

162

HAMULONEMA GEN. NOV. FOR OSTERTAGIA KENYENSIS AND TELADORSAGIA HAMATA IN THE OSTERTAGIINE FAUNA (NEMATODA: TRICHOSTRONGYLOIDEA) FROM AFRICAN UNGULATES  

Technology Transfer Automated Retrieval System (TEKTRAN)

: Hamulonema gen. nov. is proposed for Teladorsagia hamata and Ostertagia kenyensis in the ostertagiine nematode fauna found in artiodactyl hosts from Africa. Monomorphic species representing this genus are characterized by a bilaterally symmetrical and parallel synlophe in males and females, a 2-...

163

Paleorhodococcus dominicanus n. gen., n sp. (Actinobacteria) in a faecal droplet of Triatoma dominicana (Hemiptera: Reduviidae: Triatominae) in Dominican amber  

Microsoft Academic Search

Paleorhodococcus dominicanus n. gen., n sp. (Actinobacteria) is described from a faecal droplet of Triatoma dominicana (Hemiptera: Reduviidae: Triatominae) in Dominican amber. The fossil can be distinguished from the species of the closely related extant genus Rhodococcus Zopf 1891 by its spherical–ellipsoidal cocci forming substrate filaments with elementary branching, the clustering of coccoidal elements, the short filaments bearing reduced side

George Poinar Jr

2011-01-01

164

Paleorhodococcus dominicanus n. gen., n sp. (Actinobacteria) in a faecal droplet of Triatoma dominicana (Hemiptera: Reduviidae: Triatominae) in Dominican amber  

Microsoft Academic Search

Paleorhodococcus dominicanus n. gen., n sp. (Actinobacteria) is described from a faecal droplet of Triatoma dominicana (Hemiptera: Reduviidae: Triatominae) in Dominican amber. The fossil can be distinguished from the species of the closely related extant genus Rhodococcus Zopf 1891 by its spherical–ellipsoidal cocci forming substrate filaments with elementary branching, the clustering of coccoidal elements, the short filaments bearing reduced side

George Poinar Jr.

2012-01-01

165

Coynema gen. n., a new genus of nematode (Thelastomatoidea, Hystrignathidae) parasites of Passalidae (Coleoptera) from Cuba  

PubMed Central

Abstract The new genus Coynema gen. n. is described as parasite of the two passalid beetles from Cuba: Passalus interstitialis Escholtz, 1829 (type host) and Passalus pertyi Kaup, 1869. Females are characterized by the shape of their cephalic end, cervical cuticle unarmed, a sub-cylindrical procorpus with its base abruptly dilated, fore region of intestine dilated as a sac-like structure, genital system didelphic-amphidelphic and eggs markedly ovoid and smooth-shelled. Males have a digestive system similar to females, tail sharply pointed, bearing a Y-like thickening of the dorsal cuticle. They also present a big, median, mammiform pre-cloacal papillae and a pair of small, sub-dorsal pre-cloacal papillae anterior to the cuticular thickening of the tail.

Rodriguez, Jans Morffe; Rodriguez, Nayla Garcia

2011-01-01

166

Actinomycetospora chiangmaiensis gen. nov., sp. nov., a new member of the family Pseudonocardiaceae.  

PubMed

A novel actinomycete strain, YIM 0006(T), was isolated from soil of a tropical rainforest in northern Thailand. The isolate displayed the following characteristics: aerial mycelium is absent, short spore chains are formed directly on the substrate mycelium, contains meso-diaminopimelic acid, arabinose and galactose (cell-wall chemotype IV), the diagnostic phospholipid is phosphatidylcholine, MK-9(H(4)) is the predominant menaquinone and the G+C content of the genomic DNA is 69.0 mol%. Phylogenetic analysis and phenotypic characteristics showed that strain YIM 0006(T) belongs to the family Pseudonocardiaceae but can be distinguished from representatives of all genera classified in the family. The novel genus and species Actinomycetospora chiangmaiensis gen. nov., sp. nov. are proposed, with strain YIM 0006(T) (=CCTCC AA 205017(T) =DSM 45062(T)) as the type strain of Actinomycetospora chiangmaiensis. PMID:18218940

Jiang, Yi; Wiese, Jutta; Tang, Shu-Kun; Xu, Li-Hua; Imhoff, Johannes F; Jiang, Cheng-Lin

2008-02-01

167

CorGen--measuring and generating long-range correlations for DNA sequence analysis  

PubMed Central

CorGen is a web server that measures long-range correlations in the base composition of DNA and generates random sequences with the same correlation parameters. Long-range correlations are characterized by a power-law decay of the auto correlation function of the GC-content. The widespread presence of such correlations in eukaryotic genomes calls for their incorporation into accurate null models of eukaryotic DNA in computational biology. For example, the score statistics of sequence alignment and the performance of motif finding algorithms are significantly affected by the presence of genomic long-range correlations. We use an expansion-randomization dynamics to efficiently generate the correlated random sequences. The server is available at

Messer, Philipp W.; Arndt, Peter F.

2006-01-01

168

Brevifollis gellanilyticus gen. nov., sp. nov., a gellan-gum-degrading bacterium of the phylum Verrucomicrobia.  

PubMed

The taxonomic properties of strain DC2c-G4(T), a Gram-staining-negative, ovoid, gellan-gum-degrading bacterial isolate, were examined. Phylogenetic analysis based on 16S rRNA gene sequences identified this isolate as a member of the phylum Verrucomicrobia and closest to the genus Prosthecobacter. The 16S rRNA gene sequence similarities between this isolate and any of the type strains of species of the genus Prosthecobacter were less than 95 %. In addition, the absence of a single prostheca and the predominant menaquinone MK-7(H2) supported the differentiation of this isolate from the genus Prosthecobacter. Here, we propose Brevifollis gellanilyticus gen. nov., sp. nov. to accommodate the isolate. The type strain of the type species is DC2c-G4(T) (= NBRC 108608(T) = CIP 110457(T)). PMID:23416572

Otsuka, Shigeto; Suenaga, Taku; Vu, Hoan Thi; Ueda, Hiroyuki; Yokota, Akira; Senoo, Keishi

2013-02-15

169

Roseimicrobium gellanilyticum gen. nov., sp. nov., a new member of the class Verrucomicrobiae.  

PubMed

The taxonomic properties of strain DC2a-G7(T), a Gram-negative, ovoid to rod-shaped, gellan gum-lysing bacterium, were examined. The 16S rRNA gene sequence similarity showed that DC2a-G7(T) is a member of the phylum Verrucomicrobia and the closest type strain of a species with a validly published name is Verrucomicrobium spinosum DSM 4136(T), with a sequence similarity of 91.2%. In addition to this similarity value lower than 95%, the absence of prostheca, the orangey-red colony colour and the compositions of the major menaquinones and polar lipids also supported the differentiation of this bacterium from the genus Verrucomicrobium. Here, we propose the name Roseimicrobium gellanilyticum gen. nov., sp. nov. for the isolate. The type strain of Roseimicrobium gellanilyticum is DC2a-G7(T) (=NBRC 108606(T)=DSM 25532(T)). PMID:23041636

Otsuka, Shigeto; Ueda, Hiroyuki; Suenaga, Taku; Uchino, Yoshihito; Hamada, Moriyuki; Yokota, Akira; Senoo, Keishi

2012-10-05

170

The haemosporidian parasites of bats with description of Sprattiella alecto gen. nov., sp. nov.  

PubMed Central

Four species of Haemoproteidae were found in Pteropus alecto Temminck, 1837 in Queensland, Australia: i) Johnsprentia copemani, Landau et al., 2012; ii) Sprattiella alecto gen. nov., sp. nov., characterised by schizonts in the renal vessels; iii) Hepatocystis levinei, Landau et al., 1985, originally described from Pteropus poliocephalus Temminck, 1825 and, experimentally from Culicoides nubeculosus and found in this new host and for which features of the hepatic schizonts are reported; iv) gametocytes of Hepatocystis sp. which are illustrated but cannot be assigned to a known species. A tentative interpretation of phylogenetic characters of haemosporidians of bats is provided from the morphology of the gametocytes and localisation of the tissue stages with respect to recent data on the phylogeny of bats.

Landau, I.; Chavatte, J.M.; Karadjian, G.; Chabaud, A.; Beveridge, I.

2012-01-01

171

Multilamina teevani gen. et sp. nov., a microsporidian pathogen of the neotropical termite Uncitermes teevani.  

PubMed

A new genus and species of microsporidia is described from adults of the termite Uncitermes teevani (Emerson) (n. comb., formerly Armitermes teevani), collected in Ecuador. Masses of elongate, ovoid, uninucleate spores were localized to the coelomic cavity of adult workers and measured 6.29×3.33?m (fresh) and 5.83×3.00?m (fixed). These spores were individually contained within a multi-layered sporophorous vesicle and contained an isofilar polar filament with 24-28 coils. Blast-n analysis revealed that the small subunit ribosomal DNA (ssrDNA) sequence of this new species exhibited 85% identity with that of a Varimorpha species from the fire ant, Solenopsis richteri, and slightly less (78-85% identity) to a large clade of microsporidian parasites from mosquitoes and microcrustacea. The morphological and sequence data support the conclusion that Multilamina teevani gen. et sp. nov. is a novel microsporidium and distinct from any previously described genera or species. PMID:23827081

Becnel, James J; Scheffrahn, Rudolf H; Vossbrinck, Charles; Bahder, Brian

2013-07-01

172

Life cycle of Schizochytriodinium calani nov. gen. nov. spec., a dinoflagellate parasitizing copepod eggs  

NASA Astrophysics Data System (ADS)

During the Polarstern-cruise ARK IV/2 June 1987, in the Fram Strait, dinophytes parasitizing copepod eggs were observed. In the laboratory on board, vegetative reproduction was documented and re-infection of Calanus glacialis and C. hyperboreus eggs was experimentally established. During food uptake, a primary cyst produces successively several secondary cysts, all separating immediately after formation from the primary cyst. In every one of these free floating secondary cysts up to 256 dinospores are formed by palintomy. Re-infection only occurred after a “maturation time” of at least 2 days after formation of the dinospores. The life cycle is compared to that of other similar parasitic dinophyte genera: Apodinium Chatton, Chytriodinium Chatton, Dissodinium Klebs in Pascher and Myxodinium Cachon, Cachon & Bouquaheux. As the taxon under discussion does not fit in with any species or genus known so far, it is described as Schizochytriodinium calani nov. gen. nov. spec.

Elbrächter, Malte

1988-09-01

173

Gelatinomyces siamensis gen. sp. nov. (Ascomycota, Leotiomycetes, incertae sedis) on bamboo in Thailand.  

PubMed

Gelatinomyces siamensis gen. sp. nov., incertae sedis within Leotiomycetes, the Siamese jelly-ball, is described. The fungus was collected from bamboo culms and branches in Nam Nao National Park, Phetchabun, Thailand. It presents as a ping-pong ball-sized and golf ball-like gelatinous ascostroma. The asci have numerous ascospores, are thick-walled, and arise on discoid apothecia which are aggregated and clustered to form the spherical gelatinous structures. An hyphomycete asexual morph is morphologically somewhat phialophora-like, and produces red pigments. On the basis of phylogenetic analysis based on rRNA, SSU, and LSU gene sequences, the lineage is closest to Collophora rubra. However, ITS sequences place the fungus on a well-separated branch from that fungus, and the morphological and ecological differences exclude it from Collophora. PMID:23898414

Sanoamuang, Niwat; Jitjak, Wuttiwat; Rodtong, Sureelak; Whalley, Anthony J S

2013-05-14

174

Halogeometricum borinquense gen. nov., sp. nov., a novel halophilic archaeon from Puerto Rico.  

PubMed

A novel extremely halophilic archaeon was isolated from the solar salterns of Cabo Rojo, Puerto Rico. The organism is very pleomorphic, motile and requires at least 8% (w/v) NaCl to grow. Polar lipid composition revealed the presence of a novel non-sulfate-containing glycolipid and the absence of the glycerol diether analogue of phosphatidylglycerosulfate. The G + C content of the DNA is 59 mol%. On the basis of 16S rRNA sequence data, the new isolate cannot be classified in one of the recognized genera, but occupies a position that is distantly related to the genus Haloferax. All these features justify the creation of a new genus and a new species for the family Halobacteriaceae, order Halobacteriales. The name Halogeometricum borinquense gen. nov., sp. nov. is proposed. The type strain is ATCC 700274T. PMID:9828431

Montalvo-Rodríguez, R; Vreeland, R H; Oren, A; Kessel, M; Betancourt, C; López-Garriga, J

1998-10-01

175

Eremonidiopsis aggregata, gen. n., sp. n. from Cuba, the third West Indian Dioptinae (Lepidoptera, Notodontidae).  

PubMed

A new genus and species of Dioptinae (Lepidoptera, Noctuoidea, Notodontidae) is described from Cuba, this being the third taxon of the subfamily known from the West Indies. Eremonidiopsis aggregata, gen. n., sp. n., appears to be closely related to Eremonidia mirifica Rawlins & Miller from Hispaniola among members of the tribe Dioptini. Eremonidiopsis aggregata is known from two localities in the middle and western portions of the northeastern Cuban mountain range, Nipe-Sagua-Baracoa. The species inhabits low elevations (300-400 m) covered by lowland rainforest and sclerophyll rainforest. The six known specimens, all males, were part of small swarms flying near the top of an unidentified tree during the day at both collecting sites. These localities are included within protected areas, the "Pico Cristal" National Park in the West and the "Alexander von Humbolt" National Park in the East. PMID:24146561

Aguila, Rayner Núñez

2013-09-20

176

Eremonidiopsis aggregata, gen. n., sp. n. from Cuba, the third West Indian Dioptinae (Lepidoptera, Notodontidae)  

PubMed Central

Abstract A new genus and species of Dioptinae (Lepidoptera, Noctuoidea, Notodontidae) is described from Cuba, this being the third taxon of the subfamily known from the West Indies. Eremonidiopsis aggregata, gen. n., sp. n., appears to be closely related to Eremonidia mirifica Rawlins & Miller from Hispaniola among members of the tribe Dioptini. Eremonidiopsis aggregata is known from two localities in the middle and western portions of the northeastern Cuban mountain range, Nipe–Sagua–Baracoa. The species inhabits low elevations (300–400 m) covered by lowland rainforest and sclerophyll rainforest. The six known specimens, all males, were part of small swarms flying near the top of an unidentified tree during the day at both collecting sites. These localities are included within protected areas, the “Pico Cristal” National Park in the West and the “Alexander von Humbolt” National Park in the East.

Aguila, Rayner Nunez

2013-01-01

177

Preliminary Considerations of Modified 9Cr-1Mo Steel for Gen IV Nuclear Reactor Application  

SciTech Connect

Modified 9Cr-1Mo steel is currently identified as one of the leading candidate materials in the down selection for construction of the Gen IV nuclear reactor pressure vessel. Because of the stringent requirements in strength, size, safety, design life, and maintenance for the intended nuclear application, qualification of the material demands scrutiny in various aspects such as mechanical properties, data sufficiency, Codification, mechanical behavior modeling, metallurgical stability, environmental resistance, component manufacturability and transportation. In the present paper, history of the material development is briefly reviewed; requirements and challenges for the intended application are discussed; available information on the material is described. Further research and development activities are suggested to facilitate the materials selection.

Ren, Weiju [ORNL

2008-01-01

178

Removal of Collagen Nerve Conduits (NeuraGen) after Unsuccessful Implantation: Focus on Histological Findings.  

PubMed

Nerve conduits are nonneural, hollow tubular structures designed to bridge the gap of a sectioned nerve, to protect the nerve from scar formation, and to guide the regenerating fibers into the distal nerve stump. In the 8-year experience of our department, four patients aged 14 to 50 years had an unsuccessful implantation of a nerve conduit (NeuraGen, Integra, Plainsboro, NJ). In these four patients, the collagen tubes were replaced by an autogenous nerve graft. The histological specimens showed characteristic histological findings of a scar neuroma without any signs of foreign body reaction in three cases and with minimal foreign body reaction in one case. The collagen nerve tube was completely resorbed in all cases after a time period of 6 to 17 months and could not be detected marco- or microscopically.To our knowledge, this is the first report in the English and German literature describing the histological characteristics of explanted collagen nerve tubes in humans. PMID:23818251

Liodaki, Eirini; Bos, Inge; Lohmeyer, Joern A; Senyaman, Oezge; Mauss, Karl Ludwig; Siemers, Frank; Mailaender, Peter; Stang, Felix

2013-07-01

179

Multi-cusp ion source for Gen 5.5 doping system  

NASA Astrophysics Data System (ADS)

A multi-cusp ion source was designed for Nissin ion doping system "iG5" developed for GEN5.5 processes. It has many points of similarity to iG4 ion source. The extraction area and the internal volume of the plasma chamber are scaled up. And the method to obtain high current B+ beams is same as iG4 ion source. On the other hand, iG5 ion source has an added feature on the extraction system. We use new developed multi-slit extraction system to obtain stable beams with small divergence. The target boron beam current density of 1mA/cm (that is 130mA) was obtained.

Inouchi, Yutaka; Matsumoto, Takeshi; Dohi, Shojiro; Tanii, Masahiro; Takahashi, Genki; Imai, Katsuharu; Nishimura, Ippei; Tatemichi, Junichi; Konishi, Masashi; Naito, Masao

2012-11-01

180

Anindobothrium n. gen. (Eucestoda: Tetraphyllidea) inhabiting marine and freshwater potamotrygonid stingrays.  

PubMed

Anindobothrium n. gen. is proposed to accommodate Caulobothrium anacolum inhabiting Himantura schmardae from Colombia, and 2 new species, one inhabiting Potamotrygon orbigny in Brazil and the other inhabiting Paratrygon aereiba in Venezuela. Members of the new genus resemble members of Pararhinebothroides, Rhinebothroides, and Anthocephalum by having bothridia with poorly differentiated apical suckers and vasa deferentia expanded into external seminal vesicles. It further resembles Pararhinebothroides, Rhinebothroides, and Anthocephalum cairae by having vas deferens inserted near the poral rather than aporal end of the cirrus sac. The 3 species assigned to the new genus form an apparent monophyletic group, based on the possession of 3 putative synapomorphies: (1) genital pores in the anterior 1/4 of the proglottid, a trait that is unusual, but not unique, among phyllobothriids; (2) anteroventral ovarian lobes converging to the center of the proglottid, a character not previously reported for phyllobothriids; and (3) ovarian lobes comprising a loose network of digitiform processes. PMID:11426733

Marques, F P; Brooks, D R; Lasso, C A

2001-06-01

181

Proposal of Frondihabitans gen. nov. to replace the illegitimate genus name Frondicola Zhang et al. 2007.  

PubMed

The prokaryotic generic name Frondicola Zhang et al. 2007 is illegitimate because it is a later homonym of a fungal genus name Frondicola Hyde, 1992 (Fungi, Ascomycota, Sordariomycetes, Xylariomycetidae, Xylariales, Hyponectriaceae) [Principle 2 and Rule 51b(4) of the Bacteriological Code (1990 Revision)]. It is also questionable whether the genus name can be validly published. Therefore, a new genus name, Frondihabitans gen. nov., is proposed for this taxon. As a result, a new name is proposed for the type species, Frondihabitans australicus sp. nov., to replace the illegitimate combination Frondicola australicus Zhang et al. 2007. The type strain of Frondihabitans australicus is E1HC-02(T) (=JCM 13598(T) =DSM 17894(T)). PMID:19196793

Greene, Anthony C; Euzéby, Jean P; Tindall, Brian J; Patel, Bharat K C

2009-02-01

182

Tucunarella n. Gen. and other dactylogyrids (Monogenoidea) from cichlid fish (Perciformes) from Peruvian Amazonia.  

PubMed

During parasitological research on cichlid fish from the tributaries of the Amazon River around Iquitos, Peru, the following gill monogenoidean species were found: Tucunarella cichlae n. gen. and n. sp. from Cichla monoculus Spix and Agassiz; Gussevia alioides Kritsky, Thatcher, and Boeger, 1986 from Heros severus Heckel; Gussevia asota Kritsky, Thatcher, and Boeger, 1989 from Astronotus ocellatus (Agassiz); Gussevia disparoides Kritsky, Thatcher, and Boeger, 1986 from H. severus (all new geographical records) and Cichlasoma amazonarum Kullander (new host record); Gussevia longihaptor (Mizelle and Kritsky, 1969) Kritsky, Thatcher, and Boeger, 1986 and Gussevia undulata Kritsky, Thatcher, and Boeger, 1986 from C. monoculus ; Sciadicleithrum satanopercae Yamada, Takemoto, Bellay, and Pavanelli, 2008 from Satanoperca jurupari Heckel; and Sciadicleithrum variabilum (Mizelle and Kritsky, 1969) Kritsky, Thatcher, and Boeger, 1989 from C. amazonarum (new host and geographical records). Tucunarella n. gen. is proposed to accommodate a new species, Tucunarella cichlae , which is its type and only known species in the genus. The new genus is characterized by, besides a very large body size (about 1.5 mm vs. much less than 1 mm in other ancyrocephaline genera in Amazonia), a thickened tegument, 1 pair of eyes, overlapping gonads (testis dorsal to the germarium), nonarticulated male copulatory organ (MCO) and accessory piece, a coiled (counterclockwise) MCO, a dextral vaginal aperture, a haptor armed with 2 pairs of anchors (each with broad base and subequal roots, which are marginally folded), and dorsal and ventral bars and 14 hooks with protruding blunt thumbs and 2 different shapes (slender vs. slightly expanded shanks). Illustrations and data on morphological and biometric variability of individual species from different hosts are provided. The present data provide evidence of a relatively wide host specificity of gill monogenoideans parasitic in South American cichlids. PMID:20557192

Mendoza-Franco, Edgar F; Scholz, T; Rozkosná, P

2010-06-01

183

Modified CelliGen-packed bed bioreactors for hybridoma cell cultures.  

PubMed

This study describes two packed bed bioreactor configurations which were used to culture a mouse-mouse hybridoma cell line (ATCC HB-57) which produces an IgG1 monoclonal antibody. The first configuration consists of a packed column which is continuously perfused by recirculating oxygenated media through the column. In the second configuration, the packed bed is contained within a stationary basket which is suspended in the vessel of a CelliGen bioreactor. In this configuration, recirculation of the oxygenated media is provided by the CelliGen Cell Lift impeller. Both configurations are packed with disk carriers made from a non-woven polyester fabric. During the steady-state phase of continuous operation, a cell density of 10(8) cells per cm3 of bed volume was obtained in both bioreactor configurations. The high levels of productivity (0.5 gram MAb per 1 of packed bed per day) obtained in these systems demonstrates that the culture conditions achieved in these packed bed bioreactors are excellent for the continuous propagation of hybridomas using media which contains low levels (1%) of serum as well as serum-free media. These packed bed bioreactors allow good control of pH, dissolved oxygen and temperature. The media flows evenly over the cells and produces very low shear forces. These systems are easy to set up and operate for prolonged periods of time. The potential for scale-up using Fibra-cel carriers is enhanced due to the low pressure drop and low mass transfer resistance, which creates high void fraction approaching 90% in the packed bed. PMID:1369180

Wang, G; Zhang, W; Jacklin, C; Freedman, D; Eppstein, L; Kadouri, A

1992-01-01

184

Measurement of the neutron's electric form factor G(E)(n) via doubly polarized, quasi-elastic scattering at Jefferson Lab  

SciTech Connect

We determined the electric form factor of the neutron GEn via the reaction d(e,e?n)p using a longitudinally polarized electron beam and a frozen, polarized 15ND3 target at Jefferson Lab. The knocked out neutrons were detected in a segmented plastic scintillator in coincidence with the quasi-elastically scattered electrons which were tracked in Hall C's High Momentum Spectrometer. To extract GEn, we compared the experimental beam-target asymmetry with theoretical calculations based on different GEn models. We report the results of the fall 2001 run at Q2=0.5 and 1.0 (GeV/c)2.

Frank Wesselmann

2004-11-01

185

GenBank at Los Alamos: User manual, training guide, and reference manual for the OPEN LOOK[trademark] AWB  

SciTech Connect

The GenBank project at Los Alamos collects nucleotide sequence submissions from the biological research community. This work includes the processing of data received in several different forms as well as maintenance and quality control on those submissions. This manual explains the procedures involved in that work for both Los Alamos GenBank staff and off-site users. The GenBank database stores annotated DNA sequences. This manual contains the procedures for depositing these sequences into the database. There are two ways to do this. Either the sequence arrives at GenBank as a submission and is entered by the database staff or the sequence is directly entered by an off-site user. The Annotator's WorkBench (AWB), which is a database browsing and editing tool, is used in both cases. This manual is for GenBank staff and off-site users of the GenBank database at the Los Alamos National Laboratory. It contains an introduction and tutorials for AWB, as well as procedures for entering sequences either as submissions or as data directly deposited by an off-site user. Instructions for all of these are found in Chapters 2 through 4. The introduction to AWB is in Chapter 2. Instructions for submission handling are in Chapter 3. Instructions for entering sequence information are in Chapter 4. Off-site users should look at section 4.3 for instructions on entering a sequence. In addition, the manual describes various in-house curatorial tasks that are part of maintaining the database, as well as the procedures and conventions for annotating sequences. The procedures for annotation and review are in Chapters 5 and 6. The description of in-house curator's tasks is in Chapter 7. The appendices contain: Annotation conventions, two reference chapters on AWB and other utility programs, a complete list of all the forms, fields, and commands in AWB and descriptions of other (non-AWB) software utilities used by database staff.

Reese, G.C.; Keen, G.M.; Gilna, P.; Cinkosky, M.J.

1993-03-15

186

GenBank at Los Alamos: User manual, training guide, and reference manual for the ASCII AWB  

SciTech Connect

The GenBank project at Los Alamos collects nucleotide sequence submissions from the biological research community. This work includes the processing of data received in several different forms as well as maintenance and quality control on those submissions. This manual explains the procedures involved in that work for both Los Alamos GenBank staff and off-site users. The GenBank database stores annotated DNA sequences. This manual contains the procedures for depositing these sequences into the database. There are two ways to do this. Either the sequence arrives at GenBank as a submission and is entered by the database staff or the sequence is directly entered by an off-site user. The Annotator's WorkBench (AWB), which is a database browsing and editing tool, is used in both cases. This manual is for GenBank staff and off-site users of the GenBank database at the Los Alamos National Laboratory. It contains an introduction and tutorials for AWB, as well as procedures for entering sequences either as submissions or as data directly deposited by an off-site user. Instructions for all of these are found in Chapters 2 through 4. The introduction to AWB is in Chapter 2. Instructions for submission handling are in Chapter 3. Instructions for entering sequence information are in Chapter 4. Off-site users should look at section 4.3 for instructions on entering a sequence. In addition, the manual describes various in-house curatorial tasks that are part of maintaining the database, as well as the procedures and conventions for annotating sequences. The procedures for annotation and review are in Chapters 5 and 6. The description of in-house curator's tasks is in Chapter 7. The appendices contain: Annotation conventions, two reference chapters on AWB and other utility programs, a complete list of all the forms, fields, and commands in AWB and descriptions of other (non-AWB) software utilities used by database staff.

Reese, G.C.; Keen, G.M.; Gilna, P.; Cinkosky, M.J.

1993-03-15

187

Parvibaculum lavamentivorans gen. nov., sp. nov., a novel heterotroph that initiates catabolism of linear alkylbenzenesulfonate.  

PubMed

Strain DS-1T is a small (0.8 microm in length and 0.2 microm in diameter) heterotrophic bacterium able to omega-oxygenate the commercial surfactant linear alkylbenzenesulfonate (LAS) and shorten the side chain by beta-oxidation to yield sulfophenylcarboxylates. The morphotype is widespread in cultures able to utilize LAS, and a second organism with similar characteristics, strain AN-8, is now available. Utilization of LAS is concomitant with formation of a biofilm, and cells were non-motile. Many surfactants were utilized. The organisms also grew with acetate or octane, but required no biofilm and were motile. Analysis of the gene encoding 16S rRNA placed the organisms in the alpha-subclass of the Proteobacteria with a sequence divergence of >8 % from any species whose name has been validly published. 16S rRNA gene sequence comparison with entries in the GenBank database showed 98 % similarity to an alpha-protobacterial marine isolate, JP57: strain JP57 displayed the same morphotype as strain DS-1T, but it was unable to utilize surfactants or any single source of carbon tested. The lipid components of strains DS-1T and JP57 were virtually identical. The fatty acids contained ester- and putative amide-linked hydroxy fatty acids, in a combination that is currently unique in the alpha-Proteobacteria. The major respiratory quinone present in both strains was Q11. The polar lipids consisted of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and two unidentified aminolipids. Data on the 16S rRNA gene sequence and the lipid composition indicated that strains DS-1T and JP57 should be placed in a new genus, for which the name Parvibaculum is proposed. The differences between these strains, supported by DNA hybridizations, lead to the conclusion that strain DS-1T (= DSM 13023T = NCIMB 13966T) is the type strain of a species in the genus Parvibaculum, for which the name Parvibaculum lavamentivorans gen. nov., sp. nov. is proposed. PMID:15388700

Schleheck, David; Tindall, Brian J; Rosselló-Mora, Ramón; Cook, Alasdair M

2004-09-01

188

Air Traffic Control Modernization: Management Challenges Associated with Program Costs and Schedules Could Hinder NextGen Implementation. Report to Congressional Committees.  

National Technical Information Service (NTIS)

The Federal Aviation Administration (FAA), partnering with other federal agencies and the aviation industry, is implementing the Next Generation Air Transportation System (NextGen), a new satellite-based air traffic management system that will replace the...

2012-01-01

189

Phenotype-Genotype Integrator (PheGenI): synthesizing genome-wide association study (GWAS) data with existing genomic resources.  

PubMed

Rapidly accumulating data from genome-wide association studies (GWASs) and other large-scale studies are most useful when synthesized with existing databases. To address this opportunity, we developed the Phenotype-Genotype Integrator (PheGenI), a user-friendly web interface that integrates various National Center for Biotechnology Information (NCBI) genomic databases with association data from the National Human Genome Research Institute GWAS Catalog and supports downloads of search results. Here, we describe the rationale for and development of this resource. Integrating over 66?000 association records with extensive single nucleotide polymorphism (SNP), gene, and expression quantitative trait loci data already available from the NCBI, PheGenI enables deeper investigation and interrogation of SNPs associated with a wide range of traits, facilitating the examination of the relationships between genetic variation and human diseases.European Journal of Human Genetics advance online publication, 22 May 2013; doi:10.1038/ejhg.2013.96. PMID:23695286

Ramos, Erin M; Hoffman, Douglas; Junkins, Heather A; Maglott, Donna; Phan, Lon; Sherry, Stephen T; Feolo, Mike; Hindorff, Lucia A

2013-05-22

190

Notomegarhynchus navonae n. gen. and n. sp. (Eucestoda: Tetraphyllidea), from skates (Rajidae: Arhynchobatinae) in the southern hemisphere.  

PubMed

Notomegarhynchus n. gen. (Eucestoda: Tetraphyllidea) is proposed to accommodate Notomegarhynchus navonae n. gen., n. sp. from Atlantoraja castelnaui in Mar del Plata, Argentina. Notomegarhynchus shetlandicum n. comb. from Bathyraja eatonii and B. maccaini in South Shetlands region, Antarctica, is a second species in the genus. Notomegarhynchus belongs to the Echeneibothriinae within the Phyllobothriidae. It can be distinguished from all other tetraphyllidean genera by the structure of the scolex in form of a massive myzorhynchus consisting of a proscolex and an apical organ, both of which are nonretractable and noninvaginable; in addition, there are 4 pedunculated and nonloculate acetabula. Notomegarhynchus shetlandicum is differentiated from N. navonae particularly in details of acetabular and myzorhynchus morphology, arrangement of testes, and shape of eggs. The inclusion of Notomegarhynchus in the Echeneibothriinae requires emendation of the diagnosis of the subfamily to include taxa possessing postvaginal testes. In addition, new terminology is proposed for distinct regions of the scolex. PMID:12054009

Ivanov, Verónica A; Campbell, Ronald A

2002-04-01

191

New Australian stiletto flies: revision of Manestella Metz and description of Medomega gen. n. (Diptera, Therevidae, Agapophytinae)  

PubMed Central

Abstract The previously monotypic genus Manestella Metz, 2003 is revised with a single species, Manestella tristriata (Mann, 1933), redescribed and an additional 14 new species described: Manestella caesia sp. n., Manestella campestris sp. n., Manestella canities sp. n., Manestella cooloola sp. n., Manestella fumosa sp. n., Manestella incompleta sp. n., Manestella nubis sp. n., Manestella obscura sp. n., Manestella ocellaris sp. n., Manestella persona sp. n., Manestella poecilothorax sp. n., Manestella umbrapennis sp. n., Manestella vasta sp. n. and Manestella vespera sp. n. The putative sister genus to Manestella, Medomega gen. n., is described containing six new species: Medomega averyi sp. n., Medomega bailmeup sp. n., Medomega chlamydos sp. n., Medomega danielsi sp. n., Medomega gigasathe sp. n., and Medomega nebrias sp. n. Complete taxonomic descriptions were generated from a character matrix developed in Lucid Builder from which natural language descriptions (NLD) were parsed. Images of all species of Manestella and Medomega gen. n. are included, along with dichotomous keys to species.

Winterton, Shaun L.; Lambkin, Christine L.

2012-01-01

192

Evaluation of the GenBank, EzTaxon, and BIBI Services for Molecular Identification of Clinical Blood Culture Isolates That Were Unidentifiable or Misidentified by Conventional Methods  

PubMed Central

We compared the 16S rRNA gene sequencing results analyzed with the GenBank, EzTaxon, and BIBI databases for blood culture specimens for which identifications were incomplete, conflicting, or unidentifiable using conventional methods. Analyses performed using GenBank combined with EzTaxon (kappa = 0.79) were more discriminative than those using other databases alone or in combination with a second database.

Park, Kyung Sun; Ki, Chang-Seok; Kang, Cheol-In; Kim, Yae-Jean; Chung, Doo Ryeon; Peck, Kyong Ran; Song, Jae-Hoon

2012-01-01

193

Thermoterrabacterium ferrireducens gen. nov., sp. nov., a thermophilic anaerobic dissimilatory Fe(III)-reducing bacterium from a continental hot spring  

Microsoft Academic Search

A strain of a thermophilic, anaerobic, dissimilatory, Fe(III)-reducing bacterium, Thermoterrabacterium ferrireducens gen. nov., sp. nov. (type strain JW\\/AS-Y7{sup T}; DSM 11255), was isolated from hot springs in Yellowstone National Park and New Zealand. The gram-positive-staining cells occurred singly or in pairs as straight to slightly curved rods, 0.3 to 0.4 by 1.6 to 2.7 μm, with rounded ends and exhibited

ALEXANDER SLOBODKIN; J. Wiegel; A. L. Reysenbach

1997-01-01

194

The impact of message appeal and message source on Gen Y consumers' attitudes and purchase intentions toward American Apparel  

Microsoft Academic Search

A 3 × 2 experimental design was used to examine the impact of message appeal (fair labor, sex, or a combination of fair labor and sex) and message source (company advertisements or third-party publicity) upon Gen Y consumers' (N = 258) intent to patronize the retailer, American Apparel. Results supported models of hierarchical effects of advertising on patronage intention as well as the inclusion

Ruoh-Nan Yan; Jennifer Paff Ogle; Karen H. Hyllegard

2010-01-01

195

Protomonimia kasai-nakajhongii gen. et sp. nov.: A permineralized magnolialean fructification from the mid-Cretaceous of japan  

Microsoft Academic Search

Protomonimia kasai-nakajhongii gen. et sp. nov., is an angiosperm fructification with numerous helically arranged follicles attached to a concave receptacle.\\u000a It was obtained from the mid-Cretaceous (Turonian) of Hokkaido, Japan. Each follicle is a conduplicate carpel with an adaxial\\u000a stigmatic crest. It shows many primitive features of early angiosperms, especially of the Magnoliales.Protomonimia is thought to represent a member of

Harufumi Nishida; Makoto Nishida

1988-01-01

196

New evidence of reproductive organs of Glossopteris based on permineralized fossils from Queensland, Australia. I. Ovulate organ Homevaleia gen. nov  

Microsoft Academic Search

This study describes Homevaleia gouldii H. Nishida, Pigg, Kudo et Rigby gen. et sp. nov., an ovule-bearing glossopterid organ, based on a combination of recently\\u000a collected permineralized specimens from the Late Permian Homevale Station locality in the Bowen Basin of Queensland, Australia,\\u000a and on previously studied material from the 1977 Gould and Delevoryas study. Homevaleia, which resembles the compression–impression genus

Harufumi Nishida; Kathleen B. Pigg; Kensuke Kudo; John F. Rigby

2007-01-01

197

Accuracy evaluation of ClimGen weather generator and daily to hourly disaggregation methods in tropical conditions  

Microsoft Academic Search

Daily and sub-daily weather data are often required for hydrological and environmental modeling. Various weather generator\\u000a programs have been used to generate synthetic climate data where observed climate data are limited. In this study, a weather\\u000a data generator, ClimGen, was evaluated for generating information on daily precipitation, temperature, and wind speed at four\\u000a tropical watersheds located in Hawai‘i, USA. We

Mohammad Safeeq; Ali Fares

198

Riserius pugetensis gen. n., sp. n. (Nemertina: Anopla), a new mesopsammic species, and comments on phylogenetics of some anoplan characters  

Microsoft Academic Search

Riserius pugetensis gen. n., sp. n. is described from the northwest coast of Washington, U.S.A. It is probably a heteronemertine and, as such,\\u000a would be the first known mesopsammic member of that order; it lives in the interstices of medium to coarse, moderately clean\\u000a sands. Its morphology presents some attributes considered characteristic of mesopsammic fauna. The effect of some of

Jon L. Norenburg

1993-01-01

199

Zymobacter palmae gen. nov., sp. nov., a new ethanol-fermenting peritrichous bacterium isolated from palm sap  

Microsoft Academic Search

Zymobacter palmae gen. nov., sp. nov. was proposed for a new ethanol-fermenting bacterium that was isolated from palm sap in Okinawa Prefecture, Japan. The bacterium is gram-negative, facultatively anaerobic, catalase-positive, oxidase-negative, nonspore-forming and peritrichously flagellated. It requires nicotinic acid for growth. It ferments hexoses, ?-linked di- and tri-saccarides, and sugar alcohols (fructose, galactose, glucose, mannose, maltose, melibiose, saccharose, raffinose, mannitol

Tomoyuki Okamoto; Hiroshi Taguchi; Katsumi Nakamura; Hiroshi Ikenaga; Hiroshi Kuraishi; Kazuhide Yamasato

1993-01-01

200

The use of the NextGen model atmospheres for cool giants in a light curve synthesis code  

NASA Astrophysics Data System (ADS)

We have written a light curve synthesis code that makes direct use of model atmosphere specific intensities, in particular the NextGen model atmosphere grid for cool giants (Teff<= 6800 K and log (g)<= 3.5, Hauschildt et al. \\cite{hauschildt99}). We point out that these models (computed using spherical geometry) predict a limb darkening behaviour that deviates significantly from a simple linear or two-parameter law (there is less intensity at the limb of the star). The presence of a significantly nonlinear limb darkening law has two main consequences. First, the ellipsoidal light curve computed for a tidally distorted giant using the NextGen intensities is in general different from the light curve computed using the same geometry but with the black body approximation and a one- or two-parameter limb darkening law. In most cases the light curves computed with the NextGen intensities have deeper minima than their black body counterparts. Thus the light curve solutions for binaries with a giant component obtained with models with near linear limb darkening (either black body or plane-parallel model atmosphere intensities) are biased. Observations over a wide wavelength range (i.e. both the optical and infrared) are particularly useful in discriminating between models with nearly linear limb darkening and the NextGen models. Second, we show that rotational broadening kernels for Roche lobe filling (or nearly filling) giants can be significantly different from analytic kernels due to a combination of the nonspherical shape of the star and the radical departure from a simple limb darkening law. As a result, geometrical information inferred from Vrot sin i measurements of cool giants in binary systems are likewise biased.

Orosz, J. A.; Hauschildt, P. H.

2000-12-01

201

Mycosis of bandedwinged whitefly (Trialeurodes abutilonea) (Homoptera: aleyrodidae) caused by Orthomyces aleyrodis gen. & sp. nov. (Entomophthorales: Entomophthoraceae).  

PubMed

A new genus and species of fungus, Orthomyces aleyrodis Steinkraus, Humber & Oliver gen. & sp. nov. (Entomophthorales: Entomophthoraceae) is described. In 1994 and 1995, this fungus caused epizootics in high populations of bandedwinged whitefly (Trialeurodes abutilonea) on cotton and cocklebur in Alabama. In 1996, T. abutilonea populations were lower and no infected specimens were found. This is the first report of an entomophthoralean infecting an aleyrodid in the New World and the first report of entomophthoralean epizootics in whiteflies. PMID:9647695

Steinkraus, D C; Oliver, J B; Humber, R A; Gaylor, M J

1998-07-01

202

Kretzoiarctos gen. nov., the Oldest Member of the Giant Panda Clade  

PubMed Central

The phylogenetic position of the giant panda, Ailuropoda melanoleuca (Carnivora: Ursidae: Ailuropodinae), has been one of the most hotly debated topics by mammalian biologists and paleontologists during the last century. Based on molecular data, it is currently recognized as a true ursid, sister-taxon of the remaining extant bears, from which it would have diverged by the Early Miocene. However, from a paleobiogeographic and chronological perspective, the origin of the giant panda lineage has remained elusive due to the scarcity of the available Miocene fossil record. Until recently, the genus Ailurarctos from the Late Miocene of China (ca. 8–7 mya) was recognized as the oldest undoubted member of the Ailuropodinae, suggesting that the panda lineage might have originated from an Ursavus ancestor. The role of the purported ailuropodine Agriarctos, from the Miocene of Europe, in the origins of this clade has been generally dismissed due to the paucity of the available material. Here, we describe a new ailuropodine genus, Kretzoiarctos gen. nov., based on remains from two Middle Miocene (ca. 12–11 Ma) Spanish localities. A cladistic analysis of fossil and extant members of the Ursoidea confirms the inclusion of the new genus into the Ailuropodinae. Moreover, Kretzoiarctos precedes in time the previously-known, Late Miocene members of the giant panda clade from Eurasia (Agriarctos and Ailurarctos). The former can be therefore considered the oldest recorded member of the giant panda lineage, which has significant implications for understanding the origins of this clade from a paleobiogeographic viewpoint.

Abella, Juan; Alba, David M.; Robles, Josep M.; Valenciano, Alberto; Rotgers, Cheyenn; Carmona, Raul; Montoya, Plinio; Morales, Jorge

2012-01-01

203

Kretzoiarctos gen. nov., the oldest member of the giant panda clade.  

PubMed

The phylogenetic position of the giant panda, Ailuropoda melanoleuca (Carnivora: Ursidae: Ailuropodinae), has been one of the most hotly debated topics by mammalian biologists and paleontologists during the last century. Based on molecular data, it is currently recognized as a true ursid, sister-taxon of the remaining extant bears, from which it would have diverged by the Early Miocene. However, from a paleobiogeographic and chronological perspective, the origin of the giant panda lineage has remained elusive due to the scarcity of the available Miocene fossil record. Until recently, the genus Ailurarctos from the Late Miocene of China (ca. 8-7 mya) was recognized as the oldest undoubted member of the Ailuropodinae, suggesting that the panda lineage might have originated from an Ursavus ancestor. The role of the purported ailuropodine Agriarctos, from the Miocene of Europe, in the origins of this clade has been generally dismissed due to the paucity of the available material. Here, we describe a new ailuropodine genus, Kretzoiarctos gen. nov., based on remains from two Middle Miocene (ca. 12-11 Ma) Spanish localities. A cladistic analysis of fossil and extant members of the Ursoidea confirms the inclusion of the new genus into the Ailuropodinae. Moreover, Kretzoiarctos precedes in time the previously-known, Late Miocene members of the giant panda clade from Eurasia (Agriarctos and Ailurarctos). The former can be therefore considered the oldest recorded member of the giant panda lineage, which has significant implications for understanding the origins of this clade from a paleobiogeographic viewpoint. PMID:23155439

Abella, Juan; Alba, David M; Robles, Josep M; Valenciano, Alberto; Rotgers, Cheyenn; Carmona, Raül; Montoya, Plinio; Morales, Jorge

2012-11-14

204

Geofilum rubicundum gen. nov., sp. nov., isolated from deep subseafloor sediment.  

PubMed

A novel, facultatively anaerobic bacterium (strain JAM-BA0501(T)) was isolated from a deep subseafloor sediment sample at a depth of 247 m below seafloor off the Shimokita Peninsula of Japan in the north-western Pacific Ocean (Site C9001, 1180 m water depth). Cells of strain JAM-BA0501(T) were gram-negative, filamentous, non-spore-forming and motile on solid medium by gliding. Phylogenetic analysis based on the 16S rRNA gene sequence of strain JAM-BA0501(T) indicated a distant relationship to strains representing genera within the order Bacteroidales, such as Alkaliflexus imshenetskii Z-7010(T) (91.1?% similarity), Marinilabilia salmonicolor ATCC 19041(T) (86.2?%) and Anaerophaga thermohalophila Fru22(T) (89.3?%). The new isolate produced isoprenoid quinones with menaquinone MK-7 as the major component, and the predominant fatty acids were iso-C(15?:?0) and anteiso-C(15?:?0). The DNA G+C content of the isolate was 42.9 mol%. Based on its taxonomic distinctiveness, strain JAM-BA0501(T) is considered to represent a novel species of a new genus within the family Marinilabiliaceae, for which the name Geofilum rubicundum gen. nov., sp. nov. is proposed. The type strain of Geofilum rubicundum is JAM-BA0501(T) (?=?JCM 15548(T) ?=?NCIMB 14482(T)). PMID:21705444

Miyazaki, Masayuki; Koide, Osamu; Kobayashi, Tohru; Mori, Kozue; Shimamura, Shigeru; Nunoura, Takuro; Imachi, Hiroyuki; Inagaki, Fumio; Nagahama, Takahiko; Nogi, Yuichi; Deguchi, Shigeru; Takai, Ken

2011-06-24

205

Litorimicrobium taeanense gen. nov., sp. nov., isolated from a sandy beach.  

PubMed

A Gram-reaction-negative, strictly aerobic, non-motile bacterium, designated strain G4(T), was isolated from a sandy beach of Taean in South Korea. Cells were ovoid rods and were catalase- and oxidase-positive. Growth of strain G4(T) was determined at 15-35 °C (optimum 25-30 °C) and pH 6-8 (optimum pH 6.5-7.5). Strain G4(T) contained Q-10 as the predominant isoprenoid quinone and C(18 : 1)?7c (59.0 %), C(18 : 1)?7c 11-methyl (11.3 %) and C(12 : 1) 3-OH (9.8 %) as the major fatty acids. The major cellular polar lipids were identified as phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, an unidentified amino lipid, an unidentified phospholipid and an unidentified lipid. The DNA G+C content was 62.4 mol%. Phylogenetic and comparative analysis based on 16S rRNA gene sequences indicated that strain G4(T) fell within the family Rhodobacteraceae of Alphaproteobacteria and was most closely related to members of the genera Marinovum, Leisingera and Phaeobacter with 95.5-96.4 % sequence similarities. On the basis of phenotypic, chemotaxonomic and molecular properties, strain G4(T) represents a novel species of a novel genus within the family Rhodobacteraceae, for which the name Litorimicrobium taeanense gen. nov., sp. nov. is proposed. The type strain is G4(T) (?=?KACC 13706(T) ?=?DSM 22007(T)). PMID:20639225

Jin, Hyun Mi; Lee, Hyo Jung; Kim, Jeong Myeong; Park, Moon Su; Lee, Kangseok; Jeon, Che Ok

2010-07-16

206

Rubricoccus marinus gen. nov., sp. nov., of the family 'Rhodothermaceae', isolated from seawater.  

PubMed

A coccoid- and amorphous-shaped, non-gliding, reddish bacterium, designated SG-29(T), was isolated from seawater in the western North Pacific Ocean near Japan. The strain was Gram-stain-negative, obligately aerobic, heterotrophic and catalase-positive. Nitrate was reduced to nitrogen and acid was produced from aesculin, turanose, 2-keto-gluconate and arabinose. Growth occurred with 1-5?% NaCl (optimum 2?% NaCl) and at 5-37 °C (optimum 20-30 °C). The G+C content of genomic DNA was 68.9 mol% (HPLC). The predominant isoprenoid quinone was MK-7 and the major cellular fatty acids (>10?%) were iso-C??:??9c, C??:??8c and iso-C??:?. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SG-29(T) belonged to the phylum Bacteroidetes. The most closely related strain was Rhodothermus obamensis JCM 9785(T), with which the isolate exhibited 86.1?% 16S rRNA gene sequence similarity. On the basis of phenotypic and phylogenetic features, strain SG-29(T) is classified in a novel genus and species within the family 'Rhodothermaceae', for which the name Rubricoccus marinus gen. nov., sp. nov. (?=?NBRC 107124(T) ?=?KCTC 23197(T)) is proposed. PMID:20851913

Park, Sanghwa; Yoshizawa, Susumu; Kogure, Kazuhiro; Yokota, Akira

2010-09-17

207

A new captorhinid reptile, Gansurhinus qingtoushanensis, gen. et sp. nov., from the Permian of China.  

PubMed

Captorhinids, a clade of Paleozoic reptiles, are represented by a rich fossil record that extends from the Late Carboniferous into the Late Permian. Representatives of this clade dispersed from the equatorial regions of Laurasia into the temperate regions of Pangea during the Middle and Late Permian. This rich fossil record shows that there was an evolutionary trend from faunivorous to omnivorous and herbivorous feeding habits within this clade. The discovery of well-preserved captorhinid materials in the Middle Permian of China allows us to determine that the new taxon, Gansurhinus qingtoushanensis, gen. et sp. nov, is a member of Moradisaurinae, a clade of captorhinids with multiple tooth rows arranged in parallel. The presence of this moradisaurine in the Middle Permian of south central Asia leads us to suggest that paleogeographic changes during the Permian, with part of what is today China becoming a large peninsula of Pangea, allowed these early reptiles as well as other terrestrial vertebrates to extend their geographic ranges to this region of the Late Paleozoic supercontinent. PMID:21484260

Reisz, Robert R; Liu, Jun; Li, Jin-Ling; Müller, Johannes

2011-04-12

208

Emergency Decay Heat Removal in a GEN-IV Gas-Cooled Fast Reactor  

SciTech Connect

A series of transient analyses using the system code RELAP5-3d has been performed to confirm the efficacy of a proposed hybrid active/passive combination approach to the decay heat removal for an advanced 2400 MWt GEN-IV gas-cooled fast reactor. The accident sequence of interest is a station blackout simultaneous with a small break (10 sq.inch/0.645 m{sup 2}) in the reactor vessel. The analyses cover the three phases of decay heat removal in a depressurization accident: (1) forced flow cooling by the power conversion unit (PCU) coast down, (2) active forced flow cooling by a battery powered blower, and (3) passive cooling by natural circulation. The blower is part of an emergency cooling system (ECS) that by design is to sustain passive decay heat removal via natural circulation cooling 24 hours after shutdown. The RELAP5 model includes the helium-cooled reactor, the ECS (primary and secondary side), the PCU with all the rotating machinery (turbine and compressors) and the heat transfer components (recuperator, pre-cooler and inter-cooler), and the guard containment that surrounds the reactor and the PCU. The transient analysis has demonstrated the effectiveness of passive decay heat removal by natural circulation cooling when the guard containment pressure is maintained at or above 800 kPa. (authors)

Cheng, Lap Y.; Ludewig, Hans; Jo, Jae [Brookhaven National Laboratory, P.O. Box 5000, Upton, NY 11973-5000 (United States)

2006-07-01

209

Arenicella xantha gen. nov., sp. nov., a gammaproteobacterium isolated from a marine sandy sediment.  

PubMed

A Gram-negative, aerobic, yellow-pigmented, rod-shaped, non-motile bacterium, strain KMM 3895T, was isolated from a marine sandy sample collected offshore from the Sea of Japan. Phylogenetic analysis based on the 16S rRNA gene sequence placed strain KMM 3895T in the class Gammaproteobacteria, forming a separate branch, sharing 89.5 % sequence similarity with Nitrincola lacisaponensis 4CAT and 88-87% similarity with the other members of the cluster, including members of Kangiella, Spongiibacter, Alcanivorax and Microbulbifer. The major isoprenoid quinone was Q-8. Polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, aminophospholipid and an unknown phospholipid. Fatty acid analysis revealed C16:1omega7, iso-C16:0, iso-C18:0 and C18:1omega7 as dominant components. The DNA G+C content was determined to be 48.1 mol%. Based on its unique phenotypic characteristics and phylogenetic distance, the marine coastal sediment isolate KMM 3895T should be classified as a representative of a novel genus and species, for which the name Arenicella xantha gen. nov., sp. nov. is proposed. The type strain of Arenicella xantha is KMM 3895T (=NRIC 0759T =JCM 16153T). PMID:19767361

Romanenko, Lyudmila A; Tanaka, Naoto; Frolova, Galina M; Mikhailov, Valery V

2009-09-18

210

Longimycelium tulufanense gen. nov., sp. nov., a filamentous actinomycete of the family Pseudonocardiaceae.  

PubMed

A novel filamentous actinomycete strain, designated TRM 46004(T), was isolated from sediment of Aiding Lake in Tulufan Basin (42° 64' N 89° 26' E), north-west China. The isolate was characterized using a polyphasic approach. The isolate formed abundant aerial mycelium with few branches and vegetative mycelium, occasionally twisted and coiled; spherical sporangia containing one to several spherical spores developed at the ends of short sporangiophores on aerial mycelium. The G+C content of the DNA was 65.2 mol%. The isolate contained meso-diaminopimelic acid as the diagnostic diamino acid and xylose, galactose and ribose as the major whole-cell sugars. The diagnostic phospholipids were phosphatidylethanolamine, phosphatidylcholine and phosphatidylglycerol. The predominant menaquinones were MK-9(H4), MK-9(H6) and MK-9(H10). The major fatty acids were iso-C16 : 0 and anteiso-C17 : 0. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain TRM 46004(T) formed a distinct lineage within the family Pseudonocardiaceae and showed 91.7-96.1 % 16S rRNA gene sequence similarity with members of the family Pseudonocardiaceae. On the basis of the evidence from this polyphasic study, a novel genus and species, Longimycelium tulufanense gen. nov., sp. nov., are proposed. The type strain of Longimycelium tulufanense is TRM 46004(T) (= CGMCC 4.5737(T) = NBRC 107726(T)). PMID:23315412

Xia, Zhan-Feng; Guan, Tong-Wei; Ruan, Ji-Sheng; Huang, Ying; Zhang, Li-Li

2013-01-11

211

Sergeia podlipaevi gen. nov., sp. nov. (Trypanosomatidae, Kinetoplastida), a parasite of biting midges (Ceratopogonidae, Diptera).  

PubMed

Three strains of a trypanosomatid protozoan were isolated from the midguts of two naturally infected species of biting midges [Culicoides (Oecacta) festivipennis and Culicoides (Oecacta) truncorum] and characterized by light and electron microscopy and by molecular techniques. Morphological characteristics and sequences of the 18S rRNA, 5S rRNA, spliced leader RNA and glycosomal glyceraldehyde-3-phosphate dehydrogenase genes indicate that the studied flagellates represent a novel phylogenetic lineage within the Trypanosomatidae. Based on phylogenetic analyses, the novel endosymbiont-free, monoxenous trypanosomatid was classified as Sergeia podlipaevi gen. nov., sp. nov. Interestingly, it is closely related to another trypanosomatid species that parasitizes the sand fly Lutzomyia evansi, a blood-sucking dipteran from South America. The type strain of S. podlipaevi sp. nov., ICUL/CZ/2000/CER3, was obtained from Malpighian tubes. Of 2518 females of seven species of biting midges trapped in the Czech Republic, more than 1.5 % were infected by trypanosomatid parasites. An unrelated insect species, Culicoides (Monoculicoides) nubeculosus, was experimentally infected with S. podlipaevi, demonstrating that its host range extends to different subgenera of biting midges. PMID:17267991

Svobodová, Milena; Zídková, Lenka; Cepicka, Ivan; Oborník, Miroslav; Lukes, Julius; Votýpka, Jan

2007-02-01

212

Microvirga subterranea gen. nov., sp. nov., a moderate thermophile from a deep subsurface Australian thermal aquifer.  

PubMed

A strictly aerobic bacterium, strain Fail4T, was isolated from free-flowing geothermal waters of a bore (bore register no. 3768) tapping the Great Artesian Basin of Australia. The non-sporulating, Gram-negative cells of strain Fail4T produced light-pink colonies, were rod-shaped (1 x 1.5-4 microm) and were motile by a single polar flagellum. Strain Fail4T grew optimally at 41 degrees C at a pH of 7.0 and had an absolute requirement for yeast extract. The strain grew on casein hydrolysate, tryptone, gelatin, xylose and acetate in a medium supplemented with 0.06 or 0.006% yeast extract. Weak acid production was detected from glucose and arabinose. Catalase was produced. Nitrite was produced from nitrate. Strain Fail4T was sensitive to antibiotics that inhibit growth of bacteria. The G + C content was 63.5 +/- 0.5 mol%. Strain Fail4T was a member of the class 'Alphaproteobacteria', phylum Proteobacteria, placed almost equidistantly between Methylobacterium species, Chelatococcus asaccharovorans and Bosea thiooxidans (similarity value of 93%) as its nearest phylogenetic relatives. Phylogenetic and phenotypic evidence suggest that strain Fail4T (=ATCC BAA-295T = DSM 14364T) should be placed as the type strain of a species in a newly created genus, for which the name Microvirga subterranea gen. nov., sp. nov. is proposed. PMID:12710604

Kanso, Sungwan; Patel, Bharat K C

2003-03-01

213

Thiobaca trueperi gen. nov., sp. nov., a phototrophic purple sulfur bacterium isolated from freshwater lake sediment.  

PubMed

Two strains of a novel species of phototrophic micro-organism were isolated from the sediments of a shallow, freshwater, eutrophic lake. Both strains grew photolithoheterotrophically with sulfide as an electron donor, transiently accumulating intracellular sulfur globules. Photolithoautotrophic growth was not observed. One strain was designated BCH(T) (the type strain) and was studied in most detail. Cells contained bacteriochlorophyll a, and the dominant carotenoid was lycopene. Cell suspensions were brown. The photosynthetic membranes had a vesicular arrangement. Acetate, propionate, pyruvate, succinate and fumarate were each used as electron donors and carbon sources in the presence of sulfide and bicarbonate. In the presence of light, growth did not occur with hydrogen, thiosulfate or iron(II). The optimum temperature for growth was between 25 and 30 degrees C, the maximum being 36 degrees C. The G+C content of the genomic DNA of strain BCH(T) was 63 mol%. Analysis of the 16S RNA genes showed that both strains belonged to the gamma-subclass of the Proteobacteria but were phylogenetically distinct from any described phototrophic organisms within the Chromatiaceae. On the basis of phylogenetic and physiological differences from other phototrophic microorganisms, strain BCH(T) is described as a novel species of a new genus, Thiobaca trueperi gen. nov., sp. nov. PMID:11931182

Rees, Gavin N; Harfoot, Christopher G; Janssen, Peter H; Schoenborn, Liesbeth; Kuever, Jan; Lünsdorf, Heinrich

2002-03-01

214

Cohnella thermotolerans gen. nov., sp. nov., and classification of 'Paenibacillus hongkongensis' as Cohnella hongkongensis sp. nov.  

PubMed

A Gram-positive, rod-shaped, endospore-forming organism, strain CCUG 47242T, was isolated from a sample of industrial starch production in Sweden. 16S rRNA gene sequence analysis demonstrated that this isolate was moderately related to species of the genus Paenibacillus, with <94.4 % sequence similarity to all other hitherto described Paenibacillus species. Strain CCUG 47242T showed the greatest sequence similarity (96.5 %) to 'Paenibacillus hongkongensis' HKU3, a strain with a name that has not yet been validly published. Chemotaxonomic data [major menaquinone, MK-7 (98 %); major polar lipids, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, lysyl-phosphatidylglycerol, two unknown phospholipids, four unknown aminophospholipids; major fatty acids, iso-C16 : 0 and anteiso-C15 : 0] showed some significant differences when compared with the type species of the genus Paenibacillus, Paenibacillus polymyxa. Physiological and biochemical tests allowed clear phenotypic differentiation of strain CCUG 47242T from strain HKU3. On the basis of 16S rRNA gene sequence analysis, in combination with chemotaxonomic data, strains CCUG 47242T and HKU3 represent two novel species of a new genus of endospore-forming bacteria for which we propose the names Cohnella thermotolerans gen. nov., sp. nov. (type strain CCUG 47242T = CIP 108492T = DSM 17683T) and Cohnella hongkongensis sp. nov. (type strain HKU3T = CCUG 49571T = CIP 107898T = DSM 17642T). PMID:16585694

Kämpfer, Peter; Rosselló-Mora, Ramon; Falsen, Enevold; Busse, Hans-Jürgen; Tindall, Brian J

2006-04-01

215

Probing genomic diversity and evolution of Streptococcus suis serotype 2 by NimbleGen tiling arrays  

PubMed Central

Background Our previous studies revealed that a new disease form of streptococcal toxic shock syndrome (STSS) is associated with specific Streptococcus suis serotype 2 (SS2) strains. To achieve a better understanding of the pathogenicity and evolution of SS2 at the whole-genome level, comparative genomic analysis of 18 SS2 strains, selected on the basis of virulence and geographic origin, was performed using NimbleGen tiling arrays. Results Our results demonstrate that SS2 isolates have highly divergent genomes. The 89K pathogenicity island (PAI), which has been previously recognized as unique to the Chinese epidemic strains causing STSS, was partially included in some other virulent and avirulent strains. The ABC-type transport systems, encoded by 89K, were hypothesized to greatly contribute to the catastrophic features of STSS. Moreover, we identified many polymorphisms in genes encoding candidate or known virulence factors, such as PlcR, lipase, sortases, the pilus-associated proteins, and the response regulator RevS and CtsR. On the basis of analysis of regions of differences (RDs) across the entire genome for the 18 selected SS2 strains, a model of microevolution for these strains is proposed, which provides clues into Streptococcus pathogenicity and evolution. Conclusions Our deep comparative genomic analysis of the 89K PAI present in the genome of SS2 strains revealed details into how some virulent strains acquired genes that may contribute to STSS, which may lead to better environmental monitoring of epidemic SS2 strains.

2011-01-01

216

Calculation of astrophysical reaction rate of 82Ge(n,?)83Ge  

NASA Astrophysics Data System (ADS)

The neutron capture reaction on a neutron-rich near closed-shell nucleus 82Ge may play an important role in the r-process following the fallout from nuclear statistical equilibrium in core-collapse supernovae. By carrying out a DWBA analysis for the experimental angular distribution of 82Ge(d, p)83Ge reaction we obtain the single particle spectroscopic factors, S2,5/2 and S0,1/2 for the ground and first excited states of 83Ge = 82Geotimesn, respectively. And then these spectroscopic factors are used to calculate the direct capture cross sections for the 82Ge(n, ?)83Ge reaction at energies of astrophysical interest. The optical potential for neutron scattering on unstable nucleus 82Ge is not known experimentally. We employed a real folding potential which was calculated by using the proper 82Ge density distribution and an effective nucleon-nucleon force DDM3Y. The neutron capture reactions on neutron-rich closed-shell nuclei are expected to be dominated by the direct capture to bound states. We will show that the direct capture rates on these nuclei are sensitive to the structure of the low-lying states.

Wang, Mian; Chen, Yong-Shou; Li, Zhi-Hong; Liu, Wei-Ping; Shu, Neng-Chuan

2009-03-01

217

Tyrannobdella rex N. Gen. N. Sp. and the Evolutionary Origins of Mucosal Leech Infestations  

PubMed Central

Background Leeches have gained a fearsome reputation by feeding externally on blood, often from human hosts. Orificial hirudiniasis is a condition in which a leech enters a body orifice, most often the nasopharyngeal region, but there are many cases of leeches infesting the eyes, urethra, vagina, or rectum. Several leech species particularly in Africa and Asia are well-known for their propensity to afflict humans. Because there has not previously been any data suggesting a close relationship for such geographically disparate species, this unnerving tendency to be invasive has been regarded only as a loathsome oddity and not a unifying character for a group of related organisms. Principal Findings A new genus and species of leech from Perú was found feeding from the nasopharynx of humans. Unlike any other leech previously described, this new taxon has but a single jaw with very large teeth. Phylogenetic analyses of nuclear and mitochondrial genes using parsimony and Bayesian inference demonstrate that the new species belongs among a larger, global clade of leeches, all of which feed from the mucosal surfaces of mammals. Conclusions This new species, found feeding from the upper respiratory tract of humans in Perú, clarifies an expansion of the family Praobdellidae to include the new species Tyrannobdella rex n. gen. n.sp., along with others in the genera Dinobdella, Myxobdella, Praobdella and Pintobdella. Moreover, the results clarify a single evolutionary origin of a group of leeches that specializes on mucous membranes, thus, posing a distinct threat to human health.

Phillips, Anna J.; Arauco-Brown, Renzo; Oceguera-Figueroa, Alejandro; Gomez, Gloria P.; Beltran, Maria; Lai, Yi-Te; Siddall, Mark E.

2010-01-01

218

Rhodovastum atsumiense gen. nov., sp. nov., a phototrophic alphaproteobacterium isolated from paddy soil.  

PubMed

A photoorganotrophic alphaproteobacterium designated strain G2-11(T) was isolated from submerged paddy soil. This bacterium had relatively large, oval to rod-shaped cells (2.0-3.0x3.0-10 microm). Cells were motile by means of single polar flagella. The color of phototrophically growing cultures was reddish-brown. The cell extract had absorption maxima at 375, 465, 492, 529, 592, 804, and 844 nm, indicating the presence of bacteriochlorophyll a and carotenoides of the spirilloxanthin series. Vesicular intracytoplasmic membranes were present. The main component of cellular fatty acids was C(18:1)omega7c. Ubiquinone-10 and rhodoquinone-10 were the major quinones. A 16S rRNA gene sequence analysis revealed that the isolate is closest to the acidophilic aerobic photosynthetic bacterium Acidisphaera rubrifaciens strain HS-AP3(T) (93.3% similarity). The G+C content of genomic DNA is 67.8 mol%. The name Rhodovastum atsumiense gen. nov., sp. nov. is proposed for the novel isolate. The type strain is strain G2-11(T) (=NBRC 104268(T)=KCTC 5708(T)). PMID:19282632

Okamura, Keiko; Hisada, Takayoshi; Kanbe, Toshio; Hiraishi, Akira

2009-02-01

219

Durikainema macropi gen. et sp. nov. (Muspiceoidea: Robertdollfusidae). A remarkable nematode from Macropodidae (Marsupialia).  

PubMed

Durikainema macropi gen. et sp. nov. (Muspiceoidea: Robertdollfusidae) is described from the mesenteric and hepatic portal veins of Macropus giganteus Shaw 1790, M. agilis (Gould 1842) and M. rufogriseus (Desmarest 1817) (Marsupialia: Macropodidae) from Queensland, Australia. It is also known from histological sections of hepatic portal veins of M. robustus Gould 1841, M. fuliginosus (Desmarest 1817) and Lagorchestes conspicillatus Gould 1842. The new genus resembles the Enoplina in cephalic and caudal characters and the Dorylaimina in other characters. Durikainema resembles Robertdollfusa Chabaud and Campana 1950 in its small form, absence of mouth oesophagus and anus, atrophied digestive tube, reduction of female genital apparatus to a uterine pouch, viviparity and cephalic cuticular inflation in larvae. It differs from this genus in its complex and well developed cephalic structures and its well developed body musculature in both sexes. Durikainema is tentatively placed in the Robertdollfusidae, Muspiceoidea. Larvae develop beyond firststage in the uterus of the female. They have been found in the non-peripheral blood of male and female M. giganteus, the lactating mammary gland of female M. agilis but not the non-lactating glands of the same female and in the deep capillaries of thigh skin of male M. agilis. Transmission of the parasite may be direct by a percutaneous or milk route, or indirect by a haemophagous arthropod. PMID:7081889

Spratt, D M; Speare, R

1982-01-01

220

Caldalkalibacillus thermarum gen. nov., sp. nov., a novel alkalithermophilic bacterium from a hot spring in China.  

PubMed

A thermophilic, alkaliphilic and catalase-positive bacterium, designated strain HA6(T), was isolated from a hot spring in China. The strain was aerobic and chemo-organotrophic and grew optimally at 60 degrees C, pH 8.5 and 1.5 % (w/v) NaCl. The cells were Gram-positive rods, forming single terminal endospores. The predominant cellular fatty acids were iso-C(15 : 0) and iso-C(17 : 0). The cell-wall peptidoglycan contained meso-diaminopimelic acid. The genomic DNA G+C content was 45.2 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain HA6(T) formed a distinct lineage within the family Bacillaceae and was most closely related to Bacillus horti K13(T) and Bacillus smithii DSM 4216(T), with sequence similarities of 91.8 and 93.1 %, respectively. On the basis of its physiological and molecular properties, strain HA6(T) should be placed in a novel genus and species, for which the name Caldalkalibacillus thermarum gen. nov., sp. nov. is proposed. The type strain of Caldalkalibacillus thermarum is strain HA6(T) (=CGMCC 1.4242(T)=JCM 13486(T)). PMID:16738094

Xue, Yanfen; Zhang, Xinqi; Zhou, Cheng; Zhao, Yueju; Cowan, Don A; Heaphy, Shaun; Grant, William D; Jones, Brian E; Ventosa, Antonio; Ma, Yanhe

2006-06-01

221

Methanoregula boonei gen. nov., sp. nov., an acidiphilic methanogen isolated from an acidic peat bog.  

PubMed

A novel acidiphilic, hydrogenotrophic methanogen, designated strain 6A8(T), was isolated from an acidic (pH 4.0-4.5) and ombrotrophic (rain-fed) bog located near Ithaca, NY, USA. Cultures were dimorphic, containing thin rods (0.2-0.3 ?m in diameter and 0.8-3.0 ?m long) and irregular cocci (0.2-0.8 ?m in diameter). The culture utilized H(2)/CO(2) to produce methane but did not utilize formate, acetate, methanol, ethanol, 2-propanol, butanol or trimethylamine. Optimal growth conditions were near pH 5.1 and 35 °C. The culture grew in basal medium containing as little as 0.43 mM Na(+) and growth was inhibited completely by 50 mM NaCl. To our knowledge, strain 6A8(T) is one of the most acidiphilic (lowest pH optimum) and salt-sensitive methanogens in pure culture. Acetate, coenzyme M, vitamins and yeast extract were required for growth. It is proposed that a new genus and species be established for this organism, Methanoregula boonei gen. nov., sp. nov. The type strain of Methanoregula boonei is 6A8(T) (=DSM 21154(T) =JCM 14090(T)). PMID:20154331

Bräuer, Suzanna L; Cadillo-Quiroz, Hinsby; Ward, Rebekah J; Yavitt, Joseph B; Zinder, Stephen H

2010-02-12

222

Alveus, gen. nov. (Bacillariaceae, Bacillariophyta), a heavily silicified diatom found in warm water oceans.  

PubMed

Scanning electron microscope images of complete and damaged frustules of Nitzschia marina Grun. revealed an unusual chambered structure of the valve. This structure is not present in any existing nitzschioid genus and warrants an independent generic status for this taxon, which is therefore separated into Alveus gen. nov. Generic and emended specific definitions are provided and presented in the context of their relationship to other genera within the family Bacillariaceae. Deep relief of the inner surface of Alveus valves is similar to that of genera Fragilariopsis, Denticulopsis, Neodenticula, and Crucidenticula. It differs from all these diatoms in the alveolar striation. This heavily silicified diatom was found in samples from the US Joint Global Oceanographic Flux Studies cruise TT007 stations 2 and 4, (9 degrees and 5 degrees N respectively, 140 degrees W) in the equatorial Pacific. Presently, this uncommon species is restricted to warm waters. It is very common in the surface sediments of the equatorial Pacific and Indian Ocean and in the tropical and subtropical Atlantic. The sedimentary record of Alveus marinus goes back to the Middle Late Miocene (approximately 8 Ma years). PMID:8820660

Kaczmarska, I; Fryxell, G A

1996-01-01

223

Fibrisoma limi gen. nov., sp. nov., a filamentous bacterium isolated from tidal flats.  

PubMed

An orange-pigmented, Gram-staining-negative, non-motile, filament-forming, rod-shaped bacterium (BUZ 3(T)) was isolated from a coastal mud sample from the North Sea (Fedderwardersiel, Germany) and characterized taxonomically using a polyphasic approach. According to 16S rRNA gene sequence data, it belonged to the family Cytophagaceae, exhibiting low 16S rRNA gene sequence similarity (<90 %) with members of the genera Spirosoma, Rudanella and Fibrella. The DNA G+C content was 52.0 mol%. The major fatty acids were summed feature 3 (comprising C(16 : 1)?7c and/or iso-C(15 : 0) 2-OH), C(16 : 1)?5c and iso-C(17 : 0) 3-OH. The major polar lipids consisted of phosphatidylethanolamine and several aminolipids. On the basis of phenotypic, chemotaxonomic and phylogenetic data, it is proposed that strain BUZ 3(T) represents a novel genus and species, for which the name Fibrisoma limi gen. nov., sp. nov. is proposed. The type strain is BUZ 3(T) (?=?DSM 22564(T) ?=?CCUG 58137(T)). PMID:20601484

Filippini, Manuela; Kaech, Andres; Ziegler, Urs; Bagheri, Homayoun C

2010-07-02

224

Seleniivibrio woodruffii gen. nov., sp. nov., a selenate- and arsenate-respiring bacterium in the Deferribacteraceae.  

PubMed

The Gram negative, obligate anaerobic, selenate-respiring bacterium, strain S4T, was isolated from activated sludge of a wastewater treatment plant in New Jersey after enrichment with 10 mM selenate as the sole electron acceptor. In addition to its selenate respiring capability, strain S4T also respires arsenate with acetate as carbon source and electron donor. Fermentative growth was not observed. The optimum growth temperature was 37°C and optimum pH was 7. Phylogenetic analysis of the 16S rRNA gene revealed that strain S4T is a new member of the Deferribacteraceae family with Denitrovibrio acetiphilus as its closest cultivated relative with 91.5% sequence similarity. The cellular fatty acid content was composed of predominately straight-chain fatty acids, C14:0, C15:0, C16:0, C17:0, and C18:0, which distinguishes this organism from its closest relatives. The DNA G+C content was found to be 47.7 mol%. Together, these findings support that strain S4T represents a novel genus and species for which the name Seleniivibrio woodruffii gen. nov., sp. nov. is proposed. The Type strain is S4T = DSM 24984T = ATCC BAA-2290T. PMID:23625257

Rauschenbach, Ines; Posternak, Valeriya; Cantarella, Pasquale; McConnell, Jennifer; Starovoytov, Valentin; Häggblom, Max M

2013-04-26

225

Guggenheimella bovis gen. nov., sp. nov., isolated from lesions of bovine dermatitis digitalis.  

PubMed

Dermatitis digitalis is an economically important ulcerative disease of undetermined aetiology affecting the hooves of cattle. Material was examined from two independent cases of this disease in Switzerland. Cultures from the advancing front of both lesions yielded large numbers of closely related short, mesophilic, non-motile, non-spore-forming, anaerobic, proteolytic, Gram-positive rods. The 16S rRNA gene sequences of strains OMZ 913(T) and OMZ 915 were identical and indicate Tindallia magadiensis and Eubacterium saphenum as their closest relatives. Phenotypically, the novel isolates are clearly distinguished from related bacteria by protein and antigen patterns, by cellular fatty acids and by API ZYM activities. The diamino acid of the Gram-positive cell wall is ornithine and the G+C content of OMZ 913(T) DNA is 44.4 mol%. The phylogenetic distance from recognized taxa in the phylum Firmicutes is sufficient to place these bovine isolates into a novel genus and species, for which the name Guggenheimella bovis gen. nov., sp. nov. is proposed, with OMZ 913(T) (=CIP 108087(T)=DSM 15657(T)) as the type strain. PMID:15774641

Wyss, C; Dewhirst, F E; Paster, B J; Thurnheer, T; Luginbühl, A

2005-03-01

226

Kozakia baliensis gen. nov., sp. nov., a novel acetic acid bacterium in the alpha-proteobacteria.  

PubMed

Four bacterial strains were isolated from palm brown sugar and ragi collected in Bali and Yogyakarta, Indonesia, by an enrichment culture approach for acetic acid bacteria. Phylogenetic analysis based on 16S rRNA gene sequences showed that the four isolates constituted a cluster separate from the genera Acetobacter, Gluconobacter, Acidomonas, Gluconacetobacter and Asaia with a high bootstrap value in a phylogenetic tree. The isolates had high values of DNA-DNA similarity (78-100%) between one another and low values of the similarity (7-25%) to the type strains of Acetobacter aceti, Gluconobacter oxydans, Gluconacetobacter liquefaciens and Asaia bogorensis. The DNA base composition of the isolates ranged from 56.8 to 57.2 mol% G+C with a range of 0-4 mol%. The major quinone was Q-10. The isolates oxidized acetate and lactate to carbon dioxide and water, but the activity was weak, as with strains of Asaia bogorensis. The isolates differed from Asaia bogorensis strains in phenotypic characteristics. The name Kozakia baliensis gen. nov., sp. nov., is proposed for the four isolates. Strain Yo-3T (= NRIC 0488T = JCM 11301T = IFO 16664T = DSM 14400T) was isolated from palm brown sugar collected in Bali, Indonesia, and was designated as the type strain. PMID:12054243

Lisdiyanti, Puspita; Kawasaki, Hiroko; Widyastuti, Yantyati; Saono, Susono; Seki, Tatsuji; Yamada, Yuzo; Uchimura, Tai; Komagata, Kazuo

2002-05-01

227

Asaia bogorensis gen. nov., sp. nov., an unusual acetic acid bacterium in the alpha-Proteobacteria.  

PubMed

Eight Gram-negative, aerobic, rod-shaped and peritrichously flagellated strains were isolated from flowers of the orchid tree (Bauhinia purpurea) and of plumbago (Plumbago auriculata), and from fermented glutinous rice, all collected in Indonesia. The enrichment culture approach for acetic acid bacteria was employed, involving use of sorbitol medium at pH 3.5. All isolates grew well at pH 3.0 and 30 degrees C. They did not oxidize ethanol to acetic acid except for one strain that oxidized ethanol weakly, and 0.35% acetic acid inhibited their growth completely. However, they oxidized acetate and lactate to carbon dioxide and water. The isolates grew well on mannitol agar and on glutamate agar, and assimilated ammonium sulfate for growth on vitamin-free glucose medium. The isolates produced acid from D-glucose, D-fructose, L-sorbose, dulcitol and glycerol. The quinone system was Q-10. DNA base composition ranged from 59.3 to 61.0 mol% G + C. Studies of DNA relatedness showed that the isolates constitute a single species. Phylogenetic analysis based on their 16S rRNA gene sequences indicated that the isolates are located in the acetic acid bacteria lineage, but distant from the genera Acetobacter, Gluconobacter, Acidomonas and Gluconacetobacter. On the basis of the above characteristics, the name Asaia bogorensis gen. nov., sp. nov. is proposed for these isolates. The type strain is isolate 71T (= NRIC 0311T = JCM 10569T). PMID:10758893

Yamada, Y; Katsura, K; Kawasaki, H; Widyastuti, Y; Saono, S; Seki, T; Uchimura, T; Komagata, K

2000-03-01

228

Dasania marina gen. nov., sp. nov., of the order Pseudomonadales, isolated from Arctic marine sediment.  

PubMed

An obligately aerobic bacterium, strain KOPRI 20902T, was isolated from a marine sediment in Ny-Arlesund, Spitsbergen Islands, Norway. Cells were irregular rods and motile with polar monotrichous flagellum. The optimum growth temperature was 17-22 degrees . Cells grew best in pH 7.0-10.0 and 3-4% sea salts (corresponding to 2.3-3.1% NaCl). The novel strain required Ca2+ or Mg2+ in addition to NaCl for growth. Sequence analysis of 16S rRNA gene revealed that the Arctic isolate is distantly related with established species (<92.4% sequence similarity) and formed a monophyletic group with Cellvibrio, which formed a distinct phylogenetic lineage in the order Pseudomonadales. Predominant cellular fatty acids [C16:1 omega7c/15:0 iso 2OH (45.3%), C16:0 (18.4%), ECL 11.799 (11.2%), C10:0 3OH (10.4%)]; DNA G+C content (37.0 mol%); nitrate reduction to nitrogen; absence of aesculin hydrolysis, N-acetyl-beta-glucosaminidase and esterase; no assimilation of arabinose, galactose, glucose, lactose, maltose, and trehalose differentiated the strain from the genus Cellvibrio. Based on the phylogenetic and phenotypic characteristics, Dasania marina gen. nov., sp. nov. is proposed in the order Pseudomonadales. Strain KOPRI 20902T (=KCTC 12566T=JCM 13441T) is the type strain of Dasania marina. PMID:18176532

Lee, Yoo Kyung; Hong, Soon Gyu; Cho, Hyun Hee; Cho, Kyeung Hee; Lee, Hong Kum

2007-12-01

229

Katatopygia gen. n., a monophyletic branch segregated from Boletina (Diptera, Mycetophilidae)  

PubMed Central

Abstract The genus Katatopygia gen. n. is proposed for the Boletina erythropyga/punctus-group that was first introduced by Garrett (1924, 1925) and currently comprises eight described species. Molecular studies have strongly indicated that this group forms a monophyletic sister-group to a clade consisting of all other Boletina, Coelosia and Gnoriste, and its monophyly is supported by morphological data as well. The new genus includes the following species: Katatopygia antoma (Garrett, 1924), comb. n., Katatopygia antica (Garrett, 1924), comb. n., Katatopygia erythropyga (Holmgren, 1883), comb. n.,Katatopygia hissarica (Zaitzev & Polevoi, 2002), comb. n., Katatopygia magna (Garrett, 1925), comb. n., Katatopygia laticauda (Saigusa, 1968), comb. n., Katatopygia neoerythropyga (Zaitzev & Polevoi, 2002), comb. n. andKatatopygia sahlbergi (Lundström, 1906), comb. n., all transferred from Boletina. Katatopygia sahlbergi is found to be a senior synonym of Boletina punctus Garrett, 1925, syn. n. A phylogeny based on morphological data and using parsimony analysis yielded four most parsimonious trees where the new genus is retrieved as monophyletic with high support. Katatopygia neoerythropyga is found to be the sister-taxon to all other species that form two clades, one with Katatopygia sahlbergi-like species and one with Katatopygia erythropyga-like species. A key to males of Katatopygia is provided.

Martinsson, Svante; Kjaerandsen, Jostein

2012-01-01

230

Taonella mepensis gen. nov., sp. nov., a member of the family Rhodospirillaceae isolated from activated sludge.  

PubMed

A novel Gram-negative, non-spore-forming, rod-shaped strain, H1(T), was isolated from activated sludge by micromanipulation. No close relatives among cultured bacterial isolates were found; phylogenetic analysis based on 16S rRNA gene sequences revealed that strain H1(T) forms a deep single branch in the family Rhodospirillaceae. Cells of strain H1(T) were slightly curved to straight rods (1.2-1.4 × 1.5-1.7 µm) and motile by a single polar flagellum. Strain H1(T) was able to grow in the presence of 0-4 % NaCl and grew optimally at 37 °C and pH 6.0-7.0. Chemotaxonomic analysis revealed that strain H1(T) possessed Q-10 as the predominant ubiquinone and C18 : 1?7c, C16 : 0 and C19 : 0 cyclo ?8c as the major fatty acids. The DNA G+C content of strain H1(T) was 65.1 mol%. Comparative analysis of 16S rRNA gene sequences, and phenotypic and chemotaxonomic data, indicate that strain H1(T) should represent a novel genus and species of the family Rhodospirillaceae. The name Taonella mepensis gen. nov., sp. nov. is proposed. The type strain of Taonella mepensis is H1(T) ( = CICC 10529(T) = CCTCC AB 2012861(T) = KACC 16940(T)). PMID:23223814

Xi, Xue-dong; Dong, Wei-liang; Zhang, Jun; Huang, Yan; Cui, Zhong-li

2012-12-07

231

Desulfonatronovibrio hydrogenovorans gen. nov., sp. nov., an alkaliphilic, sulfate-reducing bacterium.  

PubMed

A new alkaliphilic, sulfate-reducing bacterium, strain Z-7935T (T = type strain), was isolated from a soda-depositing lake, Lake Magadi in Kenya. This organism is a motile vibrio which utilizes only hydrogen and formate as electron donors and sulfate, sulfite, and thiosulfate, but not sulfur, as electron acceptors. Thiosulfate is dismutated. Strain Z-7935T is an obligately sodium-dependent alkaliphile which grows in sodium carbonate medium and does not grow at pH 7; the maximum pH for growth is more than pH 10, and the optimum pH is 9.5 to 9.7. The optimum NaCl concentration for growth is 3% (wt/vol). The optimum temperature for growth is 37 degrees C. The G + C content of the DNA is 48.6 mol%. 16S ribosomal DNA sequence analysis revealed that strain Z-7935T represents a new lineage with genus status in the delta subclass of the Proteobacteria. The name Desulfonatronovibrio hydrogenovorans gen. nov., sp. nov. is proposed for this organism; the type strain of D. hydrogenovorans is strain Z-7935 (= DSM 9292). PMID:8995816

Zhilina, T N; Zavarzin, G A; Rainey, F A; Pikuta, E N; Osipov, G A; Kostrikina, N A

1997-01-01

232

Tubulideres seminoli gen. et sp. nov. and Zelinkaderes brightae sp. nov. (Kinorhyncha, Cyclorhagida) from Florida  

NASA Astrophysics Data System (ADS)

One new kinorhynch genus and species and one new species from the genus Zelinkaderes are described from sandy sediment off Fort Pierce, Florida. The new genus and species, Tubulideres seminoli gen. et sp. nov. is characterized by the presence of the first trunk segment consisting of a closed ring, the second segment of a bent tergal plate with a midventral articulation and the following nine segments consisting of a tergal and two sternal plates. Cuspidate spines are not present, but flexible tubules are located on several segments, and in particular concentrated on the ventral side of the second segment. Middorsal spines are present on all trunk segments and are alternatingly offset to a position slightly lateral to the middorsal line. Zelinkaderes brightae nov. sp. is characterized by its spine formula in having middorsal spines on trunk segments 4, 6 and 8-11, lateroventral acicular spines on segment 2, lateral accessory cuspidate spines on segments 2 and 8, ventrolateral cuspidate spines on segments 4-6 and 9, lateroventral acicular spines present on segments 8 and 9, and midterminal, lateral terminal and lateral terminal accessory spines on segment 11. The spine formula of Z. brightae nov. sp. places it in a position in between Z. submersus and a clade consisting of Z. klepali and Z. floridensis. The new findings on Z. brightae nov. sp. have led us to propose an emended diagnosis for the genus.

Sørensen, Martin V.; Heiner, Iben; Ziemer, Ole; Neuhaus, Birger

2007-12-01

233

Ornatilinea apprima gen. nov., sp. nov., a cellulolytic representative of the class Anaerolineae.  

PubMed

A novel obligately anaerobic, mesophilic, organotrophic bacterium, strain P3M-1(T), was isolated from a microbial mat formed in a wooden bath filled with hot water emerging from a 2775 m-deep well in the Tomsk region of western Siberia, Russia. Cells of strain P3M-1(T) were rod-shaped, 0.3-0.7 µm in width and formed multicellullar filaments that reached up to 400 µm in length. Strain P3M-1(T) grew optimally at 42-45 °C, pH 7.5-8.0, and with 0.1% (w/v) NaCl. Under optimal conditions, the doubling time was 6 h. The isolate was able to ferment a variety of proteinaceous substrates and sugars, including microcrystalline cellulose. Acetate, ethanol and H(2) were the main products of glucose fermentation. The genomic DNA G+C content was 55 mol%. 16S rRNA gene sequence-based phylogenetic analyses showed that strain P3M-1(T) was a member of the class Anaerolinea, with 92.8?% sequence similarity to Levilinea saccharolytica KIBI-1(T). Based on phylogenetic analysis and physiological properties, strain P3M-1(T) represents a novel species in a new genus, for which the name Ornatilinea apprima gen. nov., sp. nov. is proposed; the type strain of O. apprima is P3M-1(T) (= DSM 23815(T)=VKM B-2669(T)). PMID:22328612

Podosokorskaya, O A; Bonch-Osmolovskaya, E A; Novikov, A A; Kolganova, T V; Kublanov, I V

2012-02-10

234

Leisingera methylohalidivorans gen. nov., sp. nov., a marine methylotroph that grows on methyl bromide  

USGS Publications Warehouse

A marine methylotroph, designated strain MB2T, was isolated for its ability to grow on methyl bromide as a sole carbon and energy source. Methyl chloride and methyl iodide also supported growth, as did methionine and glycine betaine. A limited amount of growth was observed with dimethyl sulfide. Growth was also noted with unidentified components of the complex media marine broth 2216, yeast extract and Casamino acids. No growth was observed on methylated amines, methanol, formate, acetate, glucose or a variety of other substrates. Growth on methyl bromide and methyl iodide resulted in their oxidation to CO2 with stoichiometric release of bromide and iodide, respectively. Strain MB2T exhibited growth optima at NaCl and Mg2+ concentrations similar to that of seawater. Phylogenetic analysis of the 16S rDNA sequence placed this strain in the ??-Proteobacteria in proximity to the genera Ruegeria and Roseobacter. It is proposed that strain MB2T (= ATCC BAA-92T = DSM 14336T) be designated Leisingera methylohalidivorans gen. nov., sp. nov.

Schaefer, J. K.; Goodwin, K. D.; McDonald, I. R.; Murrell, J. C.; Oremland, R. S.

2002-01-01

235

Neoceratium gen. nov., a new genus for all marine species currently assigned to Ceratium (Dinophyceae).  

PubMed

The dinoflagellate genus Ceratium contains marine and freshwater species. Freshwater species possess six cingular plates, thick plates in the concave ventral area and usually develop a third hypothecal horn. The marine Ceratium species (>62 species) possess five cingular plates and thin plates in the concave ventral area; a third hypothecal horn is atypical. Resting cysts, a common feature in the freshwater species, are unreported in marine species. We illustrate for the first time resting cysts in marine Ceratium species (C. furca and C. candelabrum). We obtained small subunit ribosomal RNA gene (SSU rDNA) sequences of 23 Ceratium species (more than one third of the total marine species described so far), with representatives of the four acknowledged subgenera. Phylogenetic analyses including the type species, the freshwater C. hirundinella, showed that the four available sequences of freshwater species formed a strongly supported subclade, very distant from the marine cluster. Our data support the splitting of Ceratium sensu lato into two genera. Ceratium sensu stricto should be reserved for freshwater species possessing six cingular plates (three cingular plates in dorsal view). The new genus name, Neoceratium gen. nov. should be applied to the marine species of Ceratium sensu lato that possess five cingular plates (two cingular plates in dorsal view). PMID:19665427

Gómez, Fernando; Moreira, David; López-García, Purificación

2009-08-07

236

Gangjinia marincola gen. nov., sp. nov., a marine bacterium of the family Flavobacteriaceae.  

PubMed

A novel strictly aerobic, orange-pigmented, Gram-stain-negative bacterium, designated strain GJ16(T), was isolated from coastal seawater of Gangjin Bay, the southernmost part of the Korean peninsula, and subjected to a polyphasic taxonomic study. It grew optimally at 25-30 °C, at pH 7.0-8.0 and in the presence of 3?% NaCl. Comparative 16S rRNA gene sequence analysis revealed that strain GJ16(T) formed a distinct lineage within the family Flavobacteriaceae and shared less than 91.2?% 16S rRNA gene sequence similarity with members of the genera Leptobacterium, Zhouia, Winogradskyella, Dokdonia and Krokinobacter. The predominant cellular fatty acids were iso-C(15?:?0) (40.2?%), iso-C(15?:?1) G (12.8?%), iso-C(17?:?0) 3-OH (11.2?%) and C(15?:?0) (6.6?%). The G+C content of the genomic DNA was 39.4 mol% and the major respiratory isoprenoid quinone was MK-6. On the basis of phenotypic and genotypic data, strain GJ16(T) represents a novel species in a new genus in the family Flavobacteriaceae, for which the name Gangjinia marincola gen. nov., sp. nov. is proposed; the type strain is GJ16(T) (=KCTC 22649(T) =JCM 16082(T)). PMID:20228204

Lee, Dong-Heon; Moon, Sung-Ran; Park, Young-Hyun; Lee, Young Sun; Jung, Jae Sung; Kim, Jung Ho; Kim, Hoon; Kahng, Hyung-Yeel

2010-03-12

237

Fretibacterium fastidiosum gen. nov., sp. nov., isolated from the human oral cavity.  

PubMed

SGP1(T), a strain belonging to a lineage of the phylum Synergistetes with no previously cultivated representatives was subjected to a comprehensive range of phenotypic and genotypic tests. For good growth the strain was dependent on co-culture with, or extracts from, selected other oral bacteria. Cells of strain SGP1(T) were asaccharolytic and major amounts of acetic acid and moderate amounts of propionic acid were produced as end products of metabolism in peptone-yeast extract-glucose broth supplemented with a filtered cell sonicate of Fusobacterium nucleatum subsp. nucleatum ATCC 25586(T) (25?%, v/v). Hydrogen sulphide was produced and gelatin was weakly hydrolysed. The major cellular fatty acids were C(14?:?0), C(18?:?0) and C(16?:?0). The DNA G+C content of strain SGP1(T) was 63 mol%. Phylogenetic analysis of the full-length 16S rRNA gene showed that strain SGP1(T) represented a novel group within the phylum Synergistetes. A novel species in a new genus, Fretibacterium fastidiosum gen. nov., sp. nov., is proposed. The type strain of Fretibacterium fastidiosum is SGP1(T) (?=?DSM 25557(T)?=?JCM 16858(T)). PMID:22493171

Vartoukian, Sonia R; Downes, Julia; Palmer, Richard M; Wade, William G

2012-04-06

238

Aquisphaera giovannonii gen. nov., sp. nov., a planctomycete isolated from a freshwater aquarium.  

PubMed

As part of a study of the diversity of planctomycetes, two novel strains, designated OJF2(T) and OJF8, were isolated from the sediments of a freshwater aquarium. The organisms were chemoheterotrophic, spherical and pink-pigmented, had an optimum growth temperature of about 30-35 °C and an optimum pH for growth of around 7.5-8.5. The predominant fatty acids were C(18:1)?9c and C(16:0). The two strains were able to assimilate several sugars and organic acids. 16S rRNA gene sequence analysis confirmed the affiliation of these organisms to the phylum 'Planctomycetes'; they showed highest similarity to the type strains of Singulisphaera acidiphila (92.4%) and Isosphaera pallida (91.9%). On the basis of physiological, biochemical and chemotaxonomic characteristics, strains OJF2(T) and OJF8 are considered to represent a novel species of a new genus of the order Planctomycetales, for which the name Aquisphaera giovannonii gen. nov., sp. nov. is proposed. The type strain of Aquisphaera giovannonii is OJF2(T) (=CECT 7510(T) =DSM 22561(T)). PMID:21239565

Bondoso, Joana; Albuquerque, Luciana; Nobre, M Fernanda; Lobo-da-Cunha, Alexandre; da Costa, Milton S; Lage, Olga Maria

2011-01-14

239

Xiangella phaseoli gen. nov., sp. nov., a member of the family Micromonosporaceae.  

PubMed

A novel endophytic actinomycete, designated strain NEAU-J5(T) was isolated from roots of snap bean (Phaseolus vulgaris L.). Comparative analysis of the 16S rRNA gene sequence indicated that NEAU-J5(T) is phylogenetically related to members of the family Micromonosporaceae. The whole-cell sugars were galactose, mannose and glucose. The predominant menaquinones were MK-9(H4) and MK-9(H6). The major fatty acids were C16:0, C18:0, C17:1?7c, iso-C15:0 and C17:0. The phospholipids were phosphatidylmethylethanolamine, phosphatidylethanolamine, phosphatidylcholine, phosphatidylinositol and phosphatidylinositol mannoside. The DNA G+C content was 72.2 mol%. On the basis of the morphological and chemotaxonomic characteristics, phylogenetic analysis and characteristic patterns of 16S rRNA gene signature nucleotides, strain NEAU-J5(T) represents a novel species of a new genus within the family Micromonosporaceae, for which the name Xiangella phaseoli gen. nov., sp. nov. is proposed. The type strain of Xiangella phaseoli is strain NEAU-J5(T) (=CGMCC 4.7038(T)=DSM 45730(T)). PMID:23104362

Wang, Xiangjing; Jia, Feiyu; Liu, Chongxi; Zhao, Junwei; Wang, Liang; Shen, Yue; Wang, Jidong; Zhang, Ji; Li, Chuang; Xiang, Wensheng

2012-10-26

240

Sulfuricella denitrificans gen. nov., sp. nov., a sulfur-oxidizing autotroph isolated from a freshwater lake.  

PubMed

A novel facultatively anaerobic, sulfur-oxidizing bacterium, strain skB26(T), was isolated from anoxic water of a freshwater lake in Japan. The cells were rod-shaped, motile and Gram-negative. Strain skB26(T) oxidized elemental sulfur and thiosulfate to sulfate as sole energy sources. Strain skB26(T) was microaerobic and could also utilize nitrate as an electron acceptor, reducing it to nitrogen. Growth was observed at temperatures below 28 °C; optimum growth was observed at 22°C. The pH range for growth was 6.0-9.0, and the optimum pH was 7.5-8.0. Optimum growth of the isolate was observed in medium without NaCl, and no growth was observed in medium containing more than 220 mM NaCl. The G+C content of genomic DNA was around 59 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that the strain was a member of the class Betaproteobacteria, and the closest cultivated relative was 'Thiobacillus plumbophilus' DSM 6690, with 93?% sequence similarity. Phylogenetic analyses were also performed using sequences of genes involved in sulfur oxidation, inorganic carbon fixation and nitrate respiration. On the basis of its phylogenetic and phenotypic properties, strain skB26(T) (=NBRC 105220(T) =DSM 22764(T)) is proposed as the type strain of a novel species of a new genus, Sulfuricella denitrificans gen. nov., sp. nov. PMID:20081014

Kojima, Hisaya; Fukui, Manabu

2010-01-15

241

Granulibacter bethesdensis gen. nov., sp. nov., a distinctive pathogenic acetic acid bacterium in the family Acetobacteraceae.  

PubMed

A Gram-negative, aerobic, coccobacillus to rod-shaped bacterium was isolated from three patients with chronic granulomatous disease. The organism was subjected to a polyphasic taxonomic study. A multilocus phylogenetic analysis based on the 16S rRNA gene, the internal transcribed spacer (ITS) region and the RecA protein demonstrated that the organism belongs to a new sublineage within the acetic acid bacteria in the family Acetobacteraceae. Phenotypic features are summarized as follows: the organism grew at an optimum temperature of 35-37 degrees C and optimum pH of 5.0-6.5. It produced a yellow pigment, oxidized lactate and acetate, the latter weakly, produced little acetic acid from ethanol and could use methanol as a sole carbon source. The two major fatty acids were a straight-chain unsaturated acid (C18:1omega7c) and C16:0. The DNA base composition was 59.1 mol% G+C. The very weak production of acetic acid from ethanol, the ability to use methanol, the yellow pigmentation and high optimum temperature for growth distinguished this organism from other acetic acid bacteria. The unique phylogenetic and phenotypic characteristics suggest that the bacterium should be classified within a separate genus, for which the name Granulibacter bethesdensis gen. nov., sp. nov. is proposed. The type strain is CGDNIH1T (=ATCC BAA-1260T=DSM 17861T). PMID:17082400

Greenberg, David E; Porcella, Stephen F; Stock, Frida; Wong, Alexandra; Conville, Patricia S; Murray, Patrick R; Holland, Steven M; Zelazny, Adrian M

2006-11-01

242

Barrientosiimonas humi gen. nov., sp. nov., an actinobacterium of the family Dermacoccaceae.  

PubMed

Three novel actinobacteria, strains 39(T), 40 and 41, were isolated from soil collected from Barrientos Island in the Antarctic. The taxonomic status of these strains was determined using a polyphasic approach. Comparison of 16S rRNA gene sequences revealed that strain 39(T) represented a novel lineage within the family Dermacoccaceae and was most closely related to members of the genera Demetria (96.9 % 16S rRNA gene sequence similarity), Branchiibius (95.7 %), Dermacoccus (94.4-95.3 %), Calidifontibacter (94.6 %), Luteipulveratus (94.3 %), Yimella (94.2 %) and Kytococcus (93.1 %). Cells were irregular cocci and short rods. The peptidoglycan type was A4? with an L-Lys-L-Ser-D-Asp interpeptide bridge. The cell-wall sugars were galactose and glucose. The major menaquinone was MK-8(H(4)). The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphoglycolipid, two glycolipids and one unknown phospholipid. The acyl type of the cell-wall polysaccharide was N-acetyl. The major cellular fatty acids were anteiso-C(17 : 0) (41.97 %), anteiso-C(17 : 1)?9c (32.16 %) and iso-C(16 : 0) (7.68 %). The DNA G+C content of strain 39(T) was 68.4 mol%. On the basis of phylogenetic and phenotypic differences from other genera of the family Dermacoccaceae, a novel genus and species, Barrientosiimonas humi gen. nov., sp. nov., is proposed; the type strain of the type species is 39(T) (=CGMCC 4.6864(T) = DSM 24617(T)). PMID:22389286

Lee, Learn-Han; Cheah, Yoke-Kqueen; Sidik, Shiran Mohd; Xie, Qing-Yi; Tang, Yi-Li; Lin, Hai-Peng; Mutalib, Nurul-Syakima Ab; Hong, Kui

2012-03-02

243

Genea, Genabea and Gilkeya gen. nov.: ascomata and ectomycorrhiza formation in a Quercus woodland.  

PubMed

Genea and Genabea are considered ectomycorrhizal (EM) symbionts of higher plants, but because of their hypogeous habit, dark coloration and the small size of their ascomata, relatively little is known about these genera. Ascomata of six morphological species of Genea and one of Genabea were frequently collected at a single site in xeric Quercus woodlands of California's Sierra Nevada foothills. While most collections were easily referred to known species, those putatively identified as Genea harknessii and Genea arenaria were problematic. Genea harknessii collections appeared relatively homogenous based on morphology, but significant ITS variation revealed by rDNA sequencing suggested cryptic species diversity. Specimens of G. arenaria approximated the brief, original species description except for abundant clumps of septate setae formed at the apex of peridial warts. To verify the identity of this species we reexamined the holotype and analyzed morphology and ITS sequences of G. arenaria ascomata from a wide geographic range. To authenticate the EM status of Genea and Genabea with Quercus we collected healthy EM of Quercus douglasii and Quercus wislizenii and compared their ITS sequences to those from ascomata. We detected nine distinct ITS types of Genea and Genabea on roots. Two new species described here as Genea bihymeniata sp. nov. and Genea cazaresii sp. nov., were discovered during study of herbarium specimens. A phylogenetic analysis of 28 s rDNA from Genea and Genabea indicated three distinct lineages: Genea, Genabea and a third represented by Genea intermedia. For the latter we propose Gilkeya gen. nov. to accommodate the single known species, Gilkeya compacta comb. nov. A dichotomous key to all known Genea, Genabea and Gilkeya spp. from western North America is presented. PMID:17256574

Smith, Matthew E; Trappe, James M; Rizzo, David M

244

Propioniciclava tarda gen. nov., sp. nov., isolated from a methanogenic reactor treating waste from cattle farms.  

PubMed

Two facultatively anaerobic bacterial strains, designated WR061(T) and WR054, were isolated from rice-straw residue in a methanogenic reactor treating waste from cattle farms in Japan. The two strains were phylogenetically positioned close to one another and had almost the same phenotypic properties. Cells were Gram-reaction-positive, non-motile, non-spore-forming, irregular rods. Cobalamin (vitamin B??) was required for growth. The strains utilized various carbohydrates, including hexoses and disaccharides, and produced acetate and propionate from these carbohydrates. Pentoses and polysaccharides were not utilized. They grew at 20-37 °C (optimum 35 °C) and pH 5.3-8.0 (optimum pH 6.8-7.5). Catalase and nitrate-reducing activities were detected. Aesculin was hydrolysed. The major cellular fatty acids were anteiso-C??:? and C??:? DMA, the major respiratory quinone was menaquinone MK-9(H?) and the genomic DNA G+C content was 69.3-69.5 ?mol%. The diagnostic diamino acid in the peptidoglycan was meso-diaminopimelic acid. Phylogenetic analysis based on 16S rRNA gene sequences placed the strains in the phylum Actinobacteria. Both strains were remotely related to the species in the family Propionibacteriaceae and Propionibacterium propionicum JCM 5830(T) was the most closely related type strain with a sequence similarity of 91.6?%. Based on phylogenetic, physiological and chemotaxonomic analyses, the two novel strains together represent a novel species of a new genus, for which the name Propioniciclava tarda gen. nov., sp. nov. is proposed. The type strain is WR061(T) (?=?JCM 15804(T) ?=?DSM 22130(T)). PMID:20971831

Sugawara, Yoshimichi; Ueki, Atsuko; Abe, Kunihiro; Kaku, Nobuo; Watanabe, Kazuya; Ueki, Katsuji

2010-10-22

245

Analysis of first proximity voltage on the property of GEN ? image intensifier  

NASA Astrophysics Data System (ADS)

First proximity voltage is the voltage between the cathode of Low Light Level image intensifier and the input surface of Micro-channel plate?MCP?. There are so many factors influencing the image intensifier performance, and the first proximity voltage is one of the most important factors that can not be ignored. Based on the theory analysis and test of different proximity voltage on the gain?signal-to-noise ratio and equivalent background noise, this test has studied on the important performance of Gen III image intensifier effected by the proximity voltage. By the experimental study, the increase of first proximity voltage to a certain extent can improve gain?signal-to-noise ratio and equivalent background noise at the same time. The main cause of this phenomenon is that the increase of proximity voltage can enlarge the incident electron energy, and then improve the quantum efficiency of the incident electron; meantime, stray electron produced by field emission at the action of the electric field of filmed-MCP will lead to equivalent background deterioration. Ultimately we conclude that: 1) Signal to noise is proportional to the square of he cathode sensitivity, increases with the first collision energy of the incident electron, especially at 200-500ev. 2)In the increasing process of voltage from 300v to 800v, the gain of filmed-MCP increases rapidly, but lower again when Upk increases further because of gain self-saturation; lgG and lgUpk are linear relationship, thus the curve can intuitively demonstrate the relationship between them. 3) Stray electron produced by field emission at the action of the electric field of filmed-MCP will lead to equivalent background deterioration, but will not exceed the requirements of technical specifications?2.5×10-7lx?.

Zhang, Ni; Zhu, Yu-feng; Li, Dan; Nie, Jing; Zhang, Tai-min; Liu, Xiao-jian; Liu, Zhao-lu; Cheng, Wei; Fu, Ling-yun

2013-08-01

246

Pelagimonas varians gen. nov., sp. nov., isolated from the southern North Sea.  

PubMed

A heterotrophic, Gram-stain-negative, aerobic bacterium, designated strain SH4-1(T), was obtained from a seawater sample collected from the southern North Sea during a phytoplankton bloom. The 16S rRNA gene sequence comparison revealed affiliation to the Roseobacter clade (class Alphaproteobacteria) with Sulfitobacter marinus SW-265(T) as the most closely related characterized strain, showing 97.2?% 16S rRNA gene sequence similarity. Calculation of phylogenetic trees based on 16S rRNA gene sequences indicated, however, that members of the genus Roseobacter, Roseobacter denitrificans Och 114(T) and Roseobacter litoralis Och 149(T) (95?% and 96?% sequence similarity, respectively) fall between strain SH4-1(T) and the Sulfitobacter cluster including Oceanibulbus indolifex HEL-45(T) (?95.4?% sequence similarity). Cells of strain SH4-1(T) are irregular rods with at least one flagellum. Optimal growth occurred between 28 and 32 °C and at a pH between 7.0 and 8.5. Cells require the vitamin nicotinic acid amide as well as sodium ions for growth. The DNA G+C content was 55.1 mol%. The fatty acids (>1?%) comprised C10?:?0 3-OH, C12?:?1, C14?:?1 3-OH, C16?:?0, C18?:?0, C18?:?2, C18?:?1?7c and 11-methyl C18?:?1?7c. The polar lipid pattern indicated the presence of phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylmonomethylethanolamine, an unidentified aminolipid, one unidentified phospholipid and one other unidentified lipid. On the basis of phenotypic, chemotaxonomic and phylogenetic differences, strain SH4-1(T) represents a novel species in a new genus within the family Rhodobacteraceae, for which we propose the name Pelagimonas varians gen. nov., sp. nov. The type strain of the type species is SH4-1(T) (?=?DSM 23678(T)?=?LMG 26343(T)?=?CIP 110297(T)). PMID:22611199

Hahnke, Sarah; Tindall, Brian J; Schumann, Peter; Simon, Meinhard; Brinkhoff, Thorsten

2012-05-18

247

Limimonas halophila gen. nov., sp. nov., an extremely halophilic bacterium in the family Rhodospirillaceae.  

PubMed

A novel, Gram-staining-negative, non-pigmented, rod-shaped, strictly aerobic, extremely halophilic bacterium, designated strain IA16(T), was isolated from the mud of the hypersaline Lake Aran-Bidgol, in Iran. Cells of strain IA16(T) were not motile. Growth occurred with 2.5-5.2 M NaCl (optimum 3.4 M), at pH 6.0-8.0 (optimum pH 7.0) and at 30-50 °C (optimum 40 °C). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain IA16(T) belonged in the family Rhodospirillaceae and that its closest relatives were Rhodovibrio sodomensis DSM 9895(T) (91.6?% sequence similarity), Rhodovibrio salinarum NCIMB 2243(T) (91.2?%), Pelagibius litoralis CL-UU02(T) (88.9?%) and Fodinicurvata sediminis YIM D82(T) (88.7?%). The novel strain's major cellular fatty acids were C19?:?0 cyclo ?7c and C18?:?0 and its polar lipid profile comprised phosphatidylglycerol, diphosphatidylglycerol, four unidentified phospholipids, three unidentified aminolipids and two other unidentified lipids. The cells of strain IA16(T) contained the ubiquinone Q-10. The G+C content of the novel strain's genomic DNA was 67.0 mol%. The physiological, biochemical and phylogenetic differences between strain IA16(T) and other previously described taxa indicate that the strain represents a novel species in a new genus within the family Rhodospirillaceae, for which the name Limimonas halophila gen. nov., sp. nov. is proposed. The type strain of Limimonas halophila is IA16(T) (?=?IBRC-M 10018(T) ?=?DSM 25584(T)). PMID:22904212

Amoozegar, Mohammad Ali; Makhdoumi-Kakhki, Ali; Ramezani, Mohadaseh; Nikou, Mahdi Moshtaghi; Fazeli, Seyed Abolhassan Shahzadeh; Schumann, Peter; Ventosa, Antonio

2012-08-17

248

Paralcaligenes ureilyticus gen. nov., sp. nov. isolated from soil of a Korean ginseng field.  

PubMed

A bacterial strain, designated GR24-5(T), was isolated from soil cultivated with Korean ginseng. Cells were Gram-negative, strictly aerobic, catalase- and oxidase-positive, non-spore-forming motile rods. Based on the 16S rRNA gene sequence, strain GR24-5(T) could be assigned to the family Alcaligenaceae. Strain GR24-5(T) showed the highest sequence similarities with Parapusillimonas granuli Ch07(T) (97.1%), Pusillimonas noertemannii BN9(T) (96.9%), Pigmentiphaga kullae DSM 13608(T) (96.5%), and Castellaniella defragrans 54Pin(T) (96.3%). Strain GR24-5(T) demonstrated a low DNA-DNA relatedness (23%) with P. granuli Ch07(T). The major respiratory quinone is ubiquinone 8 (Q-8) and the major fatty acids are C(16:0), C(17:0) cyclo, and summed feature 1 (C(14:0) 3-OH/iso-C(16:1) I/C(12:0) aide). Putrescine, spermidine, and 2-hydroxyputrescine are the major polyamines. The major polar lipids are phosphatidylmethylethanolamine, phosphatidylethanolamine, phosphatidylglycerol, di-phosphatidylglycerol, and an unknown aminophospholipid. Polar lipid patterns of strain GR24-5(T) were unique in having a large amount of phosphatidylmethylethanolamine. Based on phylogenetic analysis and physiological and biochemical characteristics, strain GR245(T) represents a novel genus and species, for which the name Paralcaligenes ureilyticus gen. nov., sp. nov. is proposed. The type strain of P. aralcaligenes ureilyticus is GR24-5(T) (=KACC 13888 =DSM 24591(T)). PMID:21717340

Kim, Soo-Jin; Yoo, Seung-Hee; Weon, Hang-Yeon; Kim, Yi-Seul; Anandham, Rangasamy; Suh, Jang-Sun; Kwon, Soon-Wo

2011-06-30

249

Geojedonia litorea gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from coastal seawater.  

PubMed

A Gram-negative, non-flagellated, non-gliding and rod-shaped, coccoid or filamentous bacterial strain, designated YCS-16(T), was isolated from coastal seawater from a seaweed farm on the South Sea, South Korea, and its taxonomic position was investigated by using a polyphasic study. Strain YCS-16(T) was observed to grow optimally at 30 °C, at pH 7.0-7.5 and in the presence of 2 % (w/v) NaCl. Strain YCS-16(T) exhibited the highest 16S rRNA gene sequence similarity values to the type strains of Bizionia echini (96.1 %), Formosa spongicola (95.8 %), Bizionia algoritergicola (95.5 %) and Psychroserpens mesophilus (95.4 %). Neighbour-joining and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences revealed that strain YCS-16(T) joined the cluster comprising the type strains of Psychroserpens species. Strain YCS-16(T) was found to contain MK-6 as the predominant menaquinone and iso-C17:0 3-OH, iso-C15:1 G and iso-C15:0 as the major fatty acids. The major polar lipids detected in strain YCS-16(T) were phosphatidylethanolamine and one unidentified lipid. The DNA G+C content of strain YCS-16(T) was determined to be 35.7 mol%. The phylogenetic analysis, chemotaxonomic data and other phenotypic properties revealed that strain YCS-16(T) constitutes a new genus and species within the family Flavobacteriaceae, for which the name Geojedonia litorea gen. nov., sp. nov. is proposed. The type strain of Geojedonia litorea is YCS-16(T) (=KCTC 32260(T) = CCUG 63682(T)). PMID:23515678

Park, Sooyeon; Lee, Jung-Sook; Lee, Kenu-Chul; Yoon, Jung-Hoon

2013-03-21

250

Magnetovibrio blakemorei gen. nov., sp. nov., a magnetotactic bacterium (Alphaproteobacteria: Rhodospirillaceae) isolated from a salt marsh.  

PubMed

A magnetotactic bacterium, designated strain MV-1(T), was isolated from sulfide-rich sediments in a salt marsh near Boston, MA, USA. Cells of strain MV-1(T) were Gram-negative, and vibrioid to helicoid in morphology. Cells were motile by means of a single polar flagellum. The cells appeared to display a transitional state between axial and polar magnetotaxis: cells swam in both directions, but generally had longer excursions in one direction than the other. Cells possessed a single chain of magnetosomes containing truncated hexaoctahedral crystals of magnetite, positioned along the long axis of the cell. Strain MV-1(T) was a microaerophile that was also capable of anaerobic growth on some nitrogen oxides. Salinities greater than 10?% seawater were required for growth. Strain MV-1(T) exhibited chemolithoautotrophic growth on thiosulfate and sulfide with oxygen as the terminal electron acceptor (microaerobic growth) and on thiosulfate using nitrous oxide (N2O) as the terminal electron acceptor (anaerobic growth). Chemo-organoautotrophic and methylotrophic growth was supported by formate under microaerobic conditions. Autotrophic growth occurred via the Calvin-Benson-Bassham cycle. Chemo-organoheterotrophic growth was supported by various organic acids and amino acids, under microaerobic and anaerobic conditions. Optimal growth occurred at pH 7.0 and 26-28 °C. The genome of strain MV-1(T) consisted of a single, circular chromosome, about 3.7 Mb in size, with a G+C content of 52.9-53.5 mol%.Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain MV-1(T) belongs to the family Rhodospirillaceae within the Alphaproteobacteria, but is not closely related to the genus Magnetospirillum. The name Magnetovibrio blakemorei gen. nov., sp. nov. is proposed for strain MV-1(T). The type strain of Magnetovibrio blakemorei is MV-1(T) (?=?ATCC BAA-1436(T) ?=?DSM 18854(T)). PMID:22984137

Bazylinski, Dennis A; Williams, Timothy J; Lefèvre, Christopher T; Trubitsyn, Denis; Fang, Jiasong; Beveridge, Terrence J; Moskowitz, Bruce M; Ward, Bruce; Schübbe, Sabrina; Dubbels, Bradley L; Simpson, Brian

2012-09-14

251

Akkermansia muciniphila gen. nov., sp. nov., a human intestinal mucin-degrading bacterium.  

PubMed

The diversity of mucin-degrading bacteria in the human intestine was investigated by combining culture and 16S rRNA-dependent approaches. A dominant bacterium, strain MucT, was isolated by dilution to extinction of faeces in anaerobic medium containing gastric mucin as the sole carbon and nitrogen source. A pure culture was obtained using the anaerobic soft agar technique. Strain MucT was a Gram-negative, strictly anaerobic, non-motile, non-spore-forming, oval-shaped bacterium that could grow singly and in pairs. When grown on mucin medium, cells produced a capsule and were found to aggregate. Strain MucT could grow on a limited number of sugars, including N-acetylglucosamine, N-acetylgalactosamine and glucose, but only when a protein source was provided and with a lower growth rate and final density than on mucin. The G + C content of DNA from strain MucT was 47.6 mol%. 16S rRNA gene sequence analysis revealed that the isolate was part of the division Verrucomicrobia. The closest described relative of strain MucT was Verrucomicrobium spinosum (92 % sequence similarity). Remarkably, the 16S rRNA gene sequence of strain MucT showed 99 % similarity to three uncultured colonic bacteria. According to the data obtained in this work, strain MucT represents a novel bacterium belonging to a new genus in subdivision 1 of the Verrucomicrobia; the name Akkermansia muciniphila gen. nov., sp. nov. is proposed; the type strain is MucT (= ATCC BAA-835T = CIP 107961T). PMID:15388697

Derrien, Muriel; Vaughan, Elaine E; Plugge, Caroline M; de Vos, Willem M

2004-09-01

252

Rubrivirga marina gen. nov., sp. nov., a member of the family Rhodothermaceae isolated from deep seawater.  

PubMed

Two aerobic, Gram-stain-negative, pale-red-pigmented and rod-shaped bacterial strains, designated SAORIC-26 and SAORIC-28(T), were isolated from seawater (3000 m depth) from the Pacific Ocean. Phylogenetic analysis based on their 16S rRNA gene sequences revealed that the novel isolates could be affiliated with the family Rhodothermaceae of the class Cytophagia. Strains SAORIC-26 and SAORIC-28(T) shared 99.7% pairwise sequence similarity with each other and showed less than 92.6% similarity with other cultivated members of the class Cytophagia. The strains were found to be non-motile, oxidase-positive, catalase-negative and able to hydrolyse gelatin and aesculin. The DNA G+C contents were determined to be 64.8-65.8 mol% and MK-7 was the predominant menaquinone. Summed feature 9 (iso-C17:1?9c and/or C16:0 10-methyl), summed feature 3 (C16:1?6c and/or C16:1?7c) and iso-C15:0 were found to be the major cellular fatty acids. On the basis of this taxonomic study using a polyphasic approach, it was concluded that strains SAORIC-26 and SAORIC-28(T) represent a novel species of a new genus in the family Rhodothermaceae, for which the name Rubrivirga marina gen. nov., sp. nov. is proposed. The type strain of the type species of is SAORIC-28(T) (=KCTC 23867(T)=NBRC 108816(T)). An additional strain of the species is SAORIC-26. PMID:23148103

Park, Sanghwa; Song, Jaeho; Yoshizawa, Susumu; Choi, Ahyoung; Cho, Jang-Cheon; Kogure, Kazuhiro

2012-11-12

253

Gracilimonas tropica gen. nov., sp. nov., isolated from a Synechococcus culture.  

PubMed

An irregular, long, rod-shaped marine bacterium, designated CL-CB462(T), was isolated from a Synechococcus culture, which was established from surface water from the tropical Pacific Ocean. The physiological and biochemical features, fatty acid profile and phylogenetic position based on 16S rRNA gene sequences were investigated for the novel strain. Phylogenetic analysis of the 16S rRNA gene sequence showed that the closest relatives of strain CL-CB462(T) were Balneola vulgaris and Balneola alkaliphila. Strain CL-CB462(T) formed a robust clade with members of the genus Balneola in all phylogenetic trees constructed by three different methods. However, the 16S rRNA gene sequence similarity was very low (91.3-91.5 % similarity) and phenotypic and physiological features could clearly differentiate strain CL-CB462(T) from the genus Balneola. Cells of the novel strain were non-motile and spore-forming. The strain was able to grow at 1-20 % (w/v) (optimum of 3-6 %) sea salt concentration, at temperatures of 20-40 degrees C and between pH 6 and 10. The fatty acids were dominated by 15 : 0 iso (41.2 %) and 17 : 1omega9c iso (21.4 %). The DNA G+C content was 42.7 mol%. Based on polyphasic evidence, strain CL-CB462(T) was considered to represent a new genus. The name Gracilimonas tropica gen. nov., sp. nov. is proposed for the type strain of the type species (CL-CB462(T)=KCCM 90063(T)=DSM 19535(T)). PMID:19406813

Choi, Dong H; Zhang, Gwang I; Noh, Jae H; Kim, Woong-Seo; Cho, Byung C

2009-05-01

254

Halovenus aranensis gen. nov., sp. nov., an extremely halophilic archaeon from Aran-Bidgol salt lake.  

PubMed

A novel red-pigmented halophilic archaeon, strain EB27(T), was isolated from Aran-Bidgol salt lake, a hypersaline playa in Iran. Cells of strain EB27(T) were non-motile and pleomorphic (rods to triangular or disc-shaped). Strain EB27(T) required at least 2.5 M NaCl and 0.1 M MgCl(2) for growth. Optimal growth was achieved at 4 M NaCl and 0.5 M MgCl(2). The optimum pH and temperature for growth were pH 7.5 and 40 °C; it was able to grow at pH 6.0-8.0 and 25-50 °C. 16S rRNA gene sequence analysis showed that strain EB27(T) is a member of the family Halobacteriaceae; however, levels of 16S rRNA gene sequence similarity were as low as 90.0, 89.3 and 89.1 % to the most closely related haloarchaeal taxa, namely Halalkalicoccus tibetensis DS12(T), Halosimplex carlsbadense 2-9-1(T) and Halorhabdus utahensis AX-2(T), respectively. The DNA G+C content of strain EB27(T) was 61 mol%. Strain EB27(T) contained phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester, common phospholipids found in haloarchaea, together with two minor phospholipids. The only quinone present was MK-8(II-H(2)). Physiological, biochemical and phylogenetic differences between strain EB27(T) and recognized genera of extremely halophilic archaea suggest that this strain represents a novel species in a new genus within the family Halobacteriaceae, for which the name Halovenus aranensis gen. nov., sp. nov. is proposed. The type strain of Halovenus aranensis, the type species of the new genus, is strain EB27(T) ( = IBRC-M 10015(T) = CGMCC 1.11001(T)). PMID:21828022

Makhdoumi-Kakhki, A; Amoozegar, M A; Ventosa, A

2011-07-29

255

Camelimonas lactis gen. nov., sp. nov., isolated from the milk of camels.  

PubMed

Three strains of Gram-negative, rod-shaped, non-spore-forming bacteria (M 2040(T), M 1973 and M 1878-SK2), isolated from milk of camels at a camel-milk production farm in the United Arab Emirates, were investigated for their taxonomic allocation. On the basis of 16S rRNA gene sequence similarities, all three strains were shown to belong to the Alphaproteobacteria and were most closely related to Chelatococcus asaccharovorans and Chelatococcus daeguensis (95.1 and 95.2?% sequence similarity to the respective type strains). meso-Diaminopimelic acid was detected as the characteristic peptidoglycan diamino acid. The predominant compound in the polyamine pattern was spermidine, and sym-homospermidine was not detectable. The quinone system was ubiquinone Q-10. The polar lipid profile included the major compounds phosphatidylcholine and diphosphatidylglycerol and moderate amounts of phosphatidylethanolamine, phosphatidylglycerol, an unidentified glycolipid and two unidentified aminolipids. Minor lipids were also detected. The major fatty acid profile, consisting of C???:? cyclo ?8c and C??:? ?7c, with C???:?3-OH as the major hydroxylated fatty acid, was similar to those of the genus Chelatococcus. The results of DNA-DNA hybridization experiments and physiological and biochemical tests allowed both genotypic and phenotypic differentiation of the isolates from described Chelatococcus species. Isolates M 2040(T), M 1973 and M 1878-SK2 were closely related on the basis of DNA-DNA reassociation and therefore represent a single novel species. In summary, low 16S rRNA gene sequence similarities of 95?% with Chelatococcus asaccharovorans and marked differences in polar lipid profiles as well as in polyamine patterns support the description of a novel genus and species to accommodate these strains, for which the name Camelimonas lactis gen. nov., sp. nov. is proposed. The type strain of Camelimonas lactis is M 2040(T) (=CCUG 58638(T) =CCM 7696(T)). PMID:19933583

Kämpfer, P; Scholz, H C; Langer, S; Wernery, U; Wernery, R; Johnson, B; Joseph, M; Lodders, N; Busse, H-J

2009-11-20

256

Flaviflexus huanghaiensis gen. nov., sp. nov., an actinobacterium of the family Actinomycetaceae.  

PubMed

Strain H5(T) was isolated from a sediment sample collected from the coastal area of Qingdao, China. The cells were Gram-stain-positive, non-motile, straight or curved rods. The temperature range for growth was 20-37 °C and the pH for growth ranged from 6.5 to 9.0, with optimum growth occurring in the temperature range 28-30 °C and pH range 7.5-8.0. Growth occurred in the presence of 0-6% (w/v) NaCl (optimum, 0-2%). Strain H5(T) had MK-9, MK-9(H2) and MK-9(H4) as the major menaquinones and C18:1?9c, C16:0, C14:0, C18:0 and C16:1?9c as major fatty acids. The cell-wall peptidoglycan type was A5? l-Lys-l-Ala-l-Lys-d-Glu. The major polar lipids were phosphatidylglycerol (PG), an unknown phospholipid (PL1) and two unknown phosphoglycolipids (PGL1, PGL2). An unknown phospholipid (PL2) and two unknown glycolipids (GL1, GL2) were present in moderate to minor amounts in the polar lipid profile. The genomic DNA G+C content was 61.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain H5(T) represents a novel lineage in the family Actinomycetaceae. On the basis of phenotypic, physiological and molecular characteristics, it is proposed that the novel isolate should be classified as a novel species in a new genus: Flaviflexus huanghaiensis gen. nov., sp. nov., with strain H5(T) (?=?DSM 24315(T)?=CICC 10486(T)) as the type strain of the type species. PMID:23002046

Du, Zong-Jun; Miao, Ting-Ting; Lin, Xue-Zheng; Liu, Qian-Qian; Chen, Guan-Jun

2012-09-21

257

Domibacillus robiginosus gen. nov., sp. nov., isolated from a pharmaceutical clean room.  

PubMed

A novel red-pigmented bacterial strain, designated WS 4628(T), was isolated from a pharmaceutical clean room of a vaccine-producing company and was investigated in a taxonomic study using a polyphasic approach. The strain was Gram-stain-positive, strictly aerobic, motile, catalase-positive and produced spherical to slightly ellipsoidal endospores in rods. The genomic DNA G+C content was 44.1 mol%. The major fatty acids were anteiso-C15:0, iso-C15:0 and anteiso-C17:0 and the predominant quinone was MK-6. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, an unidentified phosphoglycolipid and an unidentified phospholipid. meso-diaminopimelic acid (type A1?) was present in the cell-wall peptidoglycan and the major whole-cell sugars were glucose and ribose. The closest phylogenetic neighbours were identified as Bacillus badius ATCC 14574(T) (95.8% 16S rRNA gene sequence similarity), Bacillus indicus Sd/3(T) (94.8%), Jeotgalibacillus alimentarius YKJ-13(T) (94.8%) and Bacillus cibi JG-30(T) (94.8%). Phylogenetic, physiological, biochemical and morphological differences between strain WS 4628(T) and its closest relatives in the families Bacillaceae and Planococcaceae suggest that this strain represents a novel species in a new genus in the family Bacillaceae for which the name Domibacillus robiginosus gen. nov., sp. nov. is proposed; the type strain of the type species is WS 4628(T) (=DSM 25058(T)=LMG 26645(T)). PMID:23064349

Seiler, Herbert; Wenning, Mareike; Scherer, Siegfried

2012-10-12

258

Evaluation of the Gen-Probe DNA probe for the detection of legionellae in culture  

SciTech Connect

A commercial DNA probe kit designed to detect rRNA from legionellae was evaluated for its ability to correctly discriminate between legionellae and non-legionellae taken from culture plates. The probe kit, made by the Gen-Probe Corp. (San Diego, Calif.), was radiolabeled with /sup 125/I, and probe bacterial RNA hybridization, detected in a simple one-tube system hybridization assay, was quantitated with a gamma counter. A total of 156 Legionella sp. strains were tested, of which 125 were Legionella pneumophila and the remainder were strains from 21 other Legionella spp. A total of 106 gram-negative non-legionellae, isolated from human respiratory tract (81%) and other body site (19%) specimens, were also tested; 14 genera and 28 species were represented. The probe easily distinguished all of the legionellae from the non-legionellae. The average legionellae/non-legionellae hybridization ratio was 42:1, and the lowest ratio was 2:1; a minor modification in the procedure increased the lowest ratio to 5:1. In addition to correctly identifying all Legionella species, the probe was able to separate some of the various species of Legionella. L. pneumophila strains hybridized more completely to the probe than did the other Legionella spp.; L. wadsworthii and L. oakridgensis hybridized only about 25% of the probe relative to L. pneumophila. Some strains of phenotypically identified L. pneumophila had much lower hybridization to the probe than other members of the species and may represent a new Legionella species. The simplicity of the technique and specificity of the probe make it a good candidate for confirming the identity of legionellae in culture.

Edelstein, P.H.

1986-03-01

259

Desulfatitalea tepidiphila gen. nov., sp. nov., a sulfate-reducing bacterium isolated from tidal flat sediment.  

PubMed

A novel sulfate-reducing bacterium, strain S28bF(T), was isolated from tidal flat sediment from Tokyo Bay, Japan. Cells of strain S28bF(T) were rod-shaped (0.5-0.6×1.7-3.8 µm), motile and Gram-stain-negative. For growth, the optimum pH was pH 6.8-7.3 and the optimum temperature was 34-42 °C. Strain S28bF(T) used sulfate and thiosulfate as electron acceptors, but not nitrate. The G+C content of the genomic DNA was 56.6 mol%. The fatty acid profile of strain S28bF(T) was characterized by the presence of anteiso-C(15?:?0) and C(16?:?0) as the major components. Phylogenetic analyses based on genes for 16S rRNA, the alpha subunit of dissimilatory sulfite reductase (dsrA) and adenosine-5'-phosphosulfate reductase (aprA) revealed that the isolated strain belonged to the class Deltaproteobacteria. Its closest relative was Desulfosarcina cetonica DSM 7267(T) with a 16S rRNA gene sequence similarity of 93.3?%. Two other strains, S28OL1 and S28OL2 were also isolated from the same sediment. These strains were closely related to S28bF(T) with 16S rRNA gene sequence similarities of 99?%, and the same physiological characteristics were shared with strain S28bF(T). On the basis of phylogenetic and phenotypic characterization, a novel species in a new genus, Desulfatitalea tepidiphila gen. nov., sp. nov., is proposed to accommodate the strains obtained in this study. The type strain is S28bF(T) (?=?NBRC 107166(T)?=?DSM 23472(T)). PMID:22581901

Higashioka, Yuriko; Kojima, Hisaya; Watanabe, Miho; Fukui, Manabu

2012-05-11

260

Ameyamaea chiangmaiensis gen. nov., sp. nov., an acetic acid bacterium in the alpha-Proteobacteria.  

PubMed

Two isolates, AC04(T) and AC05, were isolated from the flowers of red ginger collected in Chiang Mai, Thailand. In phylogenetic trees based on 16S rRNA gene sequences, the two isolates were included within a lineage comprised of the genera Acidomonas, Gluconacetobacter, Asaia, Kozakia, Swaminathania, Neoasaia, Granulibacter, and Tanticharoenia, and they formed an independent cluster along with the type strain of Tanticharoenia sakaeratensis. The calculated pair-wise sequence similarities of isolate AC04(T) were 97.8-92.5% to the type strains of the type species of the 11 genera of acetic acid bacteria. The DNA base composition was 66.0-66.1 mol % G+C with a range of 0.1 mol %. A single-stranded, labeled DNA from isolate AC04(T) presented levels of DNA-DNA hybridization of 100, 85, 4, and 3% respectively to DNAs from isolates AC04(T) and AC05 and the type strains of Tanticharoenia sakaeratensis and Gluconacetobacter liquefaciens. The two isolates were unique morphologically in polar flagellation and physiologically in intense acetate oxidation to carbon dioxide and water and weak lactate oxidation. The intensity in acetate oxidation almost equaled that of the type strain of Acetobacter aceti. The two isolates had Q-10. Isolate AC04(T) was discriminated from the type strains of the type species of the 11 genera by 16S rRNA gene restriction analysis using restriction endonucleases TaqI and Hin6I. The unique phylogenetic, genetic, morphological, physiological, and biochemical characteristics obtained indicate that the two isolates can be classified into a separate genus, and Ameyamaea chiangmaiensis gen. nov., sp. nov. is proposed. The type strain is isolate AC04(T) (=BCC 15744(T), =NBRC 103196(T)), which has a DNA G+C content of 66.0 mol %. PMID:19809199

Yukphan, Pattaraporn; Malimas, Taweesak; Muramatsu, Yuki; Takahashi, Mai; Kaneyasu, Mika; Potacharoen, Wanchern; Tanasupawat, Somboon; Nakagawa, Yasuyoshi; Hamana, Koei; Tahara, Yasutaka; Suzuki, Ken-ichiro; Tanticharoen, Morakot; Yamada, Yuzo

2009-10-07

261

Pleomorphobacterium xiamenense gen. nov., sp. nov., a moderate thermophile isolated from a terrestrial hot spring.  

PubMed

An aerobic, motile, moderately thermophilic rod, designated strain CLW(T), was isolated from a terrestrial hot spring in an exposition garden in Xiamen City, Fujian Province, the People's Republic of China. Strain CLW(T) formed beige, dry colonies on solid 2216E medium and flocks in liquid medium. Cells were Gram-stain-negative, short rods (1.0-3.0 µm long and 0.4-0.6 µm wide) with six or more polar flagella. The temperature and pH for growth of strain CLW(T) were 28-65 °C (optimum, 50-58 °C) and pH 5.5-9.5 (optimum, pH 6.0-8.0). Growth occurred in the presence of 0.3-6.0?% NaCl (optimum 2.5-4.5?%). Phylogenetic analysis based on 16S rRNA gene sequences showed that the closest relative of the isolate was Amaricoccus kaplicensis Ben 101(T) (94.3?% sequence similarity). The DNA G+C content of strain CLW(T) was 72.2 mol%. The respiratory quinone was ubiquinone 10. The predominant polar lipids consisted of phosphatidylglycerol and phosphatidylethanolamine. The major fatty acids (>10?%) were summed feature 8 (consisting of C18?:?1?7c and/or C18?:?1?6c), C18?:?1?7c 11-methyl and C18?:?0. Based on phylogenetic, physiological and biochemical data and DNA G+C content, strain CLW(T) is considered to represent a novel species of a new genus in the family Rhodobacteraceae, for which the name Pleomorphobacterium xiamenense gen. nov., sp. nov. is proposed. The type strain of the type species is CLW(T) (?=?LMG 26245(T)?=?CGMCC 1.10808(T)?=?MCCC 1A06272(T)). PMID:23041633

Yin, Decui; Chen, Liwei; Ao, Jingqun; Ai, Chunxiang; Chen, Xinhua

2012-10-05

262

Fonticella tunisiensis gen. nov., sp. nov., isolated from a hot spring.  

PubMed

A strictly anaerobic, moderately thermophilic, halotolerant rod, designated BELH25(T), was isolated from a water sample of a Tunisian hot spring. Cells were non-motile, 2-6 µm long and 0.4-0.6 µm wide, appearing singly or in pairs. The isolate grew at 45-70 °C (optimum 55 °C), at pH 6.2-8.0 (optimum pH 7.0) and with 0-4% NaCl (optimum 0-2.0%). Sulfate, thiosulfate, elemental sulfur, sulfite, nitrate and nitrite were not used as terminal electron acceptors. Strain BELH25(T) used cellobiose, fructose, galactose, glucose, maltose, mannose, sucrose, starch and yeast extract as electron donors. The main fermentation products from glucose metabolism were formate, acetate, ethanol and CO2. The predominant cellular fatty acids were iso-C15:0, iso-C17:0 and anteiso-C15:0. The DNA G+C content was 37.2 mol%. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain BELH25(T) was most closely related to Caloramator viterbiensis JW/MS-VS5(T) and Fervidicella metallireducens AeB(T) (92.2 and 92.1% sequence similarity, respectively), and the isolate was positioned approximately equidistantly between these genera. Based on phenotypic, phylogenetic and chemotaxonomic characteristics, strain BELH25(T) is proposed to be a member of a novel species of a novel genus within the order Clostridiales, family Clostridiaceae, for which the name Fonticella tunisiensis gen. nov., sp. nov. is proposed. The type strain of the type species is BELH25(T) (=DSM 24455(T)=JCM 17559(T)). PMID:23024143

Fraj, Belkis; Ben Hania, Wajdi; Postec, Anne; Hamdi, Moktar; Ollivier, Bernard; Fardeau, Marie-Laure

2012-09-28

263

Brockia lithotrophica gen. nov., sp. nov., an anaerobic thermophilic bacterium from a terrestrial hot spring.  

PubMed

A novel thermophilic bacterium, strain Kam1851(T), was isolated from a terrestrial hot spring of the Uzon Caldera, Kamchatka Peninsula, Russia. Cells of strain Kam1851(T) were spore-forming rods with a gram-positive type of cell wall. Growth was observed between 46 and 78 °C, and pH 5.5-8.5. The optimal growth (doubling time, 6.0 h) was at 60-65 °C and pH 6.5. The isolate was an obligate anaerobe growing in pre-reduced medium only. It grew on mineral medium with molecular hydrogen or formate as electron donors, and elemental sulfur, thiosulfate or polysulfide as electron acceptors. The main cellular fatty acids were C(16?:?0) (34.2?%), iso-C(16?:?0) (18?%), C(18?:?0) (12.8?%) and iso-C(17?:?0) (11.1?%). The G+C content of the genomic DNA of strain Kam1851(T) was 63 mol%. 16S rRNA gene sequence analysis showed that strain Kam1851(T) belonged to the order Thermoanaerobacterales, but it was not closely related to representatives of any genera with validly published names. The most closely related strains, which had no more than 89.2?% sequence similarity, were members of the genera Ammonifex and Caldanaerobacter. On the basis of its phylogenetic position and novel phenotypic features, isolate Kam1851(T) is proposed to represent a novel species in a new genus, Brockia lithotrophica gen. nov., sp. nov.; the type strain of Brockia lithotrophica is Kam1851(T) (?=?DSM 22653(T)?=?VKM B-2685(T)). PMID:22493174

Perevalova, Anna A; Kublanov, Ilya V; Baslerov, R V; Zhang, Gengxin; Bonch-Osmolovskaya, Elizaveta A

2012-04-06

264

Paenalcaligenes hominis gen. nov., sp. nov., a new member of the family Alcaligenaceae.  

PubMed

A beige-pigmented bacterium (strain CCUG 53761A(T)) was isolated from human blood from an 85-year-old man in Göteborg, Sweden. Comparative analysis of 16S rRNA gene sequences showed that this bacterium displayed <95 % similarity to all described species of the genera of the family Alcaligenaceae. It grouped within the radiation of the genus Alcaligenes, but showed only 93.0-94.8 % similarity to type strains of members of this genus (Alcaligenes faecalis subsp. parafaecalis, 94.8 %; Alcaligenes faecalis subsp. faecalis, 94.2 %; Alcaligenes faecalis subsp. phenolicus, 93.4 %). This discrimination was supported by chemotaxonomic differences. The polyamine pattern consisted of the predominant compound putrescine, moderate amounts of spermidine and minor to trace amounts of spermine and cadaverine; 2-hydroxyputrescine was not detectable. The quinone system was ubiquinone Q-8 with minor amounts of Q-7. The polar lipid profile was composed of the major lipids diphosphatidylglycerol and phosphatidylethanolamine and moderate amounts of phosphatidylglycerol and an unknown phospholipid; minor lipids were also detected. The fatty acid profile, with large amounts of C(16 : 0) and C(17 : 0) cyclo and the absence of C(12 : 0) 2-OH as hydroxylated fatty acid, also differed significantly from those reported for Alcaligenes species. On the basis of these data, it is proposed that strain CCUG 53761A(T) represents a novel genus and species, for which the name Paenalcaligenes hominis gen. nov., sp. nov. is proposed. The type strain of Paenalcaligenes hominis is CCUG 53761A(T) =CCM 7698(T). PMID:19684310

Kämpfer, P; Falsen, E; Langer, S; Lodders, N; Busse, H-J

2009-08-14

265

Edaphobacillus lindanitolerans gen. nov., sp. nov., isolated from hexachlorocyclohexane (HCH) contaminated soil.  

PubMed

A Gram-staining-positive, aerobic, cocco-bacilli-shaped, non-motile, non-spore forming, cream colored strain bacterium (strain MNA4(T) ) was isolated from hexachlorocyclohexane (HCH) contaminated soil. Strain MNA4(T) showed the highest 16S rRNA gene sequence similarity of 97.47% with type species of the newly defined genus Bhargavaea cecembensis. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain MNA4(T) belonged to a clade represented by Bhargavaea cecembensis, Bacillus beijingensis and Bacillus ginsengi. DNA-DNA hybridization values of the strain MNA4(T) with close relatives were well below the 70% threshold value recommended for delineation of species. The major fatty acids were anteiso C15:0 , anteiso C17:0 , iso C16:0 and iso C15:0 . The strain was found to contain respiratory quinones MK-8, MK-9 and MK-7 in an approximate molar ratio of 85:7:5. Polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol and two unknown phospholipids. The DNA G?+?C content was 55.6 mol%. Peptidoglycan type was A4? (L-Lys - L-Ala - D-Asp). Phylogenetic analysis, fatty acids profile, phenotypic properties and chemotaxonomic data of strain MNA4(T) indicated that it represents a novel species of a novel genus for which the name Edaphobacillus lindanitolerans gen. nov., sp. nov., is proposed. The type strain is MNA4(T) (=CCM 7584(T) ?=?DSM 22424(T) ). PMID:23322487

Lal, Devi; Khan, Fazlurrahman; Gupta, Sanjay Kumar; Schumann, Peter; Lal, Rup

2013-01-15

266

Halogranum rubrum gen. nov., sp. nov., a halophilic archaeon isolated from a marine solar saltern.  

PubMed

Two extremely halophilic archaea, strains RO2-11(T) and HO2-1, were isolated from two Chinese marine solar salterns, Rudong solar saltern and Haimen solar saltern, respectively. Cells of the two strains were polymorphic and Gram-stain-negative; colonies were red-pigmented. The two strains grew at NaCl concentrations of 2.6-4.3 M (optimum 3.9 M) and required at least 0.1 M Mg2+ for growth. They were able to grow over a pH range of 6.0-8.0 and a temperature range of 20-50 degrees C, with optimal pH of 7.5 and optimal temperature of 37 degrees C. The major polar lipids of strain RO2-11(T) and strain HO2-1 were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and three glycolipids, two of them chromatographically identical to S-DGD-1 and DGD-1, the third unidentified. The 16S rRNA gene sequence similarity of strain RO2-11(T) and strain HO2-1 was 99.3 % and highest sequence similarity with the closest relative (Haloferax larsenii) was 91.4 %. Based on the data obtained, the two isolates could not be classified in any recognized genus of the family Halobacteriaceae. Strain RO2-11(T) and strain HO2-1 are thus considered to represent a novel species of a new genus within the family Halobacteriaceae, for which the name Halogranum rubrum gen. nov., sp. nov. is proposed. The type strain is RO2-11(T) (=CGMCC 1.7738(T) =JCM 15772(T)). PMID:19671729

Cui, Heng-Lin; Gao, Xia; Sun, Fang-Fang; Dong, Ying; Xu, Xue-Wei; Zhou, Yu-Guang; Liu, Hong-Can; Oren, Aharon; Zhou, Pei-Jin

2009-08-11

267

Sulfuritalea hydrogenivorans gen. nov., sp. nov., a facultative autotroph isolated from a freshwater lake.  

PubMed

A novel facultatively autotrophic bacterium, designated strain sk43H(T), was isolated from water of a freshwater lake in Japan. Cells of the isolate were curved rods, motile and gram-reaction-negative. Strain sk43H(T) was facultatively anaerobic and autotrophic growth was observed only under anaerobic conditions. The isolate oxidized thiosulfate, elemental sulfur and hydrogen as sole energy sources for autotrophic growth and could utilize nitrate as an electron acceptor. Growth was observed at 8-32 °C (optimum 25 °C) and 6.4-7.6 (optimum pH 6.7-6.9). Optimum growth of the isolate occurred at NaCl concentrations of less than 50 mM. The G+C content of genomic DNA was around 67 mol%. The fatty acid profile of strain sk43H(T) when grown on acetate under aerobic conditions was characterized by the presence of C(16?:?0) and summed feature 3 (C(16?:?1)?7c and/or iso-C(15?:?0) 2-OH) as the major components. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain was a member of the class Betaproteobacteria showing highest sequence similarity with Georgfuchsia toluolica G5G6(T) (94.7?%) and Denitratisoma oestradiolicum AcBE2-1(T) (94.3?%). Phylogenetic analyses were also performed using genes involved in sulfur oxidation. On the basis of its phylogenetic and phenotypic properties, strain sk43H(T) (?=?DSM 22779(T) ?=?NBRC 105852(T)) represents a novel species of a new genus, for which the name Sulfuritalea hydrogenivorans gen. nov., sp. nov. is proposed. PMID:20709913

Kojima, Hisaya; Fukui, Manabu

2010-08-13

268

Proteocatella sphenisci gen. nov., sp. nov., a psychrotolerant, spore-forming anaerobe isolated from penguin guano.  

PubMed

A novel, obligately anaerobic, psychrotolerant bacterium, designated strain PPP2T, was isolated from guano of the Magellanic penguin (Spheniscus magellanicus) in Chilean Patagonia. Cells were Gram-stain-positive, spore-forming, straight rods (0.7-0.8x3.0-5.0 microm) that were motile by means of peritrichous flagella. Growth was observed at pH 6.7-9.7 (optimum pH 8.3) and 2-37 degrees C (optimum 29 degrees C). Growth was observed between 0 and 4% (w/v) NaCl with optimum growth at 0.5% (w/v). Strain PPP2T was a catalase-negative chemo-organoheterotroph that was capable of fermentative metabolism. Peptone, bacto-tryptone, Casamino acids, oxalate, starch, chitin and yeast extract were utilized as substrates. The major metabolic products were acetate, butyrate and ethanol. Strain PPP2T was resistant to ampicillin, but sensitive to tetracycline, chloramphenicol, rifampicin, kanamycin, vancomycin and gentamicin. The DNA G+C content of strain PPP2T was 39.5 mol%. Phylogenetic analysis revealed that strain PPP2T was related most closely to Clostridium sticklandii SR (approximately 90% 16S rRNA gene sequence similarity). On the basis of phylogenetic analysis and phenotypic characteristics, strain PPP2T is considered to represent a novel species of a new genus, for which the name Proteocatella sphenisci gen. nov., sp. nov. is proposed. The type strain of Proteocatella sphenisci is PPP2T (=ATCC BAA-755T=JCM 12175T=CIP 108034T). PMID:19620379

Pikuta, Elena V; Hoover, Richard B; Marsic, Damien; Whitman, William B; Lupa, Boguslaw; Tang, Jane; Krader, Paul

2009-07-20

269

Wandonia haliotis gen. nov., sp. nov., a marine bacterium of the family Cryomorphaceae, phylum Bacteroidetes.  

PubMed

A novel, strictly aerobic, Gram-stain-negative, yellow-orange-pigmented, rod-shaped bacterium was isolated from abalone (Haliotis discus) under aquaculture in seawater off the Wando coast, Southern Korea, and subjected to a polyphasic taxonomic study. Cells of strain Haldis-1(T) were catalase- and oxidase-positive rods with flexirubin pigments. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain Haldis-1(T) formed a distinct lineage within the family Cryomorphaceae and could be distinguished from the related genera Lishizhenia and Fluviicola. Strain Haldis-1(T) shared 16S rRNA gene sequence similarities of 92.5 and 92.4 % with Lishizhenia caseinilytica UST040201-001(T) and Fluviicola taffensis RW262(T), respectively. The DNA G+C content was 38.1 mol% and the major respiratory quinone was MK-7. The predominant cellular fatty acids were iso-C(15 : 0) (38.6 %), C(15 : 0) 2-OH (20.3 %) and C(15 : 0) (10.7 %). Growth was observed at 25-42 degrees C (optimum 30-37 degrees C) and at pH 6.5-9.5 (optimum pH 6.5-8.0). On the basis of polyphasic analysis of phenotypic, genotypic and phylogenetic data, strain Haldis-1(T) represents a novel genus and species within the family Cryomorphaceae in the phylum Bacteroidetes, for which the name Wandonia haliotis gen. nov., sp. nov. is proposed. The type strain is Haldis-1(T) (=KCTC 22610(T) =NBRC 105642(T)). PMID:19654361

Lee, Dong-Heon; Choi, Eun-Kyoung; Moon, Sung-Ran; Ahn, Samyoung; Lee, Young Sun; Jung, Jae Sung; Jeon, Che Ok; Whang, Kyung-Sook; Kahng, Hyung-Yeel

2009-08-04

270

Jejuia pallidilutea gen. nov., sp. nov., a new member of the family Flavobacteriaceae isolated from seawater.  

PubMed

An aerobic, pale-orange-pigmented, Gram-stain-negative bacterium, designated strain EM39T, was isolated from seawater from the eastern coast of Jeju Island, Korea, and its taxonomic status was established using a polyphasic approach. Comparative 16S rRNA gene sequence studies revealed that strain EM39T formed a distinct lineage within the family Flavobacteriaceae and could be distinguished from strains of members of the related genera Gaetbulibacter, Mariniflexile and Tamlana by 16S rRNA gene sequence analysis (similarity values between strain EM39T and related strains were all less than 93.8%). Cells of strain EM39T were non-gliding, catalase- and oxidase-positive rods that were devoid of flexirubin pigments. Growth was observed at 15-35 degrees C (optimum, 25-30 degrees C) and pH 6.5-9.0 (optimum, pH 7.0-8.5). The genomic DNA G+C content was 34.6 mol% and the major respiratory quinone was MK-6. The predominant cellular fatty acids were iso-C15:0, iso-C15:1 G and iso-C17:0 3-OH. On the basis of phenotypic and genotypic data, strain EM39T represents a novel species in a new genus in the family Flavobacteriaceae, for which the name Jejuia pallidilutea gen. nov., sp. nov. is proposed. The type strain is EM39T (=KCTC 22298T=DSM 21165T). PMID:19605703

Lee, Dong-Heon; Kahng, Hyung-Yeel; Lee, Young Sun; Jung, Jae Sung; Kim, Jeong Myeong; Chung, Bok Sil; Park, Soo Kwon; Jeon, Che Ok

2009-07-15

271

Reclassification of Agrobacterium ferrugineum LMG 128 as Hoeflea marina gen. nov., sp. nov.  

PubMed

Members of the species Agrobacterium ferrugineum were isolated from marine environments. The type strain of this species (= LMG 22047(T) = ATCC 25652(T)) was recently reclassified in the new genus Pseudorhodobacter, in the order 'Rhodobacterales' of the class 'Alphaproteobacteria'. Strain LMG 128 (= ATCC 25654) was also initially classified as belonging to the species Agrobacterium ferrugineum; however, the nearly complete 16S rRNA gene sequence of this strain indicated that it does not belong within the genus Agrobacterium or within the genus Pseudorhodobacter. The closest related organism, with 95.5 % 16S rRNA gene similarity, was Aquamicrobium defluvii from the family 'Phyllobacteriaceae' in the order 'Rhizobiales'. The remaining genera from this order had 16S rRNA gene sequence similarities that were lower than 95.1 % with respect to strain LMG 128. These phylogenetic distances suggested that strain LMG 128 belonged to a different genus. The major fatty acid present in strain LMG 128 was mono-unsaturated straight chain 18 : 1omega7c. The G + C content of the DNA was 53.1 mol%. Strain LMG 128 grew at 4 degrees C but not at 40 degrees C, and tolerated up to 5 % NaCl. The pH range for growth was 6-8. It produced urease and beta-galactosidase, and hydrolysed aesculin. Denitrification was negative. Growth was observed with many carbohydrates as the only carbon source. The data from this polyphasic study indicate that this strain belongs to a new genus of the family 'Phyllobacteriaceae', and therefore it is proposed that strain LMG 128(T) should be reclassified as representing a novel species within the new genus Hoeflea gen. nov., for which the name Hoeflea marina sp. nov. is proposed. PMID:15879249

Peix, Alvaro; Rivas, Raúl; Trujillo, Martha E; Vancanneyt, Marc; Velázquez, Encarna; Willems, Anne

2005-05-01

272

Dactylogyrids (Platyhelminthes: Monogenoidea) parasitizing butterfly fishes (Teleostei: Chaetodontidae) from the coral reefs of Palau, Moorea, Wallis, New Caledonia, and Australia: species of Euryhaliotrematoides n. gen. and Aliatrema n. gen.  

PubMed

Seven species of Euryhaliotrematoides n. gen. and 1 species of Aliatrema n. gen. (Monogenoidea; Dactylogyridae) are described and reported from the gills of 15 species of butterfly fishes (Chaetodontidae) from the coral reefs of Moorea (French Polynesia), Wallis (Wallis and Futuna), Heron and Lizard (Australia), Palau (Micronesia), and New Caledonia: Aliatrema cribbi n. sp. from Chaetodon auriga, Chaetodon lunula, Chaetodon trifasciatus, Chaetodon ulietensis, Chaetodon vagabundus, Forcipiger flavisissimus, and Heniochus chrysostomus; Euryhaliotrematoides annulocirrus n. comb. from C. auriga, C. lunula, and C. vagabundus; Euryhaliotrematoides aspistis n. sp. from C. auriga, Chaetodon citrinellus, C. lunula, Chaetodon reticulatus, C. ulietensis, and C. vagabundus; Euryhaliotrematoides berenguelae n. sp. from C. citrinellus, Chaetodon ornatissimus, and F. flavisissimus; Euryhaliotrematoides grandis n. comb. from C. auriga, C. citrinellus, Chaetodon ephippium, Chaetodon kleinii, Chaetodon lineolatus, C. lunula, C. ornatissimus, C. trifasciatus, C. vagabundus, and H. chrysostomus; Euryhaliotrematoides microphallus n. comb. from C. auriga, C. citrinellus, C. ephippium, C. kleinii, C. lunula, C. ornatissimus, C. reticulatus, Chaetodon trifascialis, C. trifasciatus, C. vagabundus, F. flavisissimus, and H. chrysostomus; Euryhaliotrematoides pirulum n. sp. from C. auriga, C. citrinellus, C. lunula, C. trifasciatus, and C. vagabundus; and Euryhaliotrematoides triangulovagina n. comb. from C. auriga, C. citrinellus, C. kleinii, C. lunula, C. ornatissimus, C. vagabundus, F. flavisissimus, H. chrysostomus, and Hemitaurichthys polylepis. All reports of previously described species are new locality records. With exceptions of E. grandis and E. annulocirrus on C. auriga and C. lunula and E. triangulovagina and E. microphallus on C. auriga, all reports are new host records. Haliotrema hainanensis and H. affinis are considered junior subjective synonyms of E. triangulovagina and E. annulocirrus, respectively. Aliatrema n. gen. is characterized by marine dactylogyrids with tandem gonads (germarium pretesticular), haptoral hooks with upright acute thumbs, a coiled copulatory organ with counterclockwise rings and funnel-shaped base but lacking an accessory piece, and a dextral vaginal pore. Euryhaliotrematoides n. gen. is characterized by marine dactylogyrids having tandem gonads (germarium pretesticular), haptoral hooks with upright acute thumbs, a coiled copulatory organ with counterclockwise rings and funnel-shaped base, a vas deferens looping the left intestinal cecum, and a dextral vaginal pore. PMID:15165056

Plaisance, Laetitia; Kritsky, Delane C

2004-04-01

273

An outlook on the fungal internal transcribed spacer sequences in GenBank and the introduction of a web-based tool for the exploration of fungal diversity.  

PubMed

The environmental and distributional data associated with fungal internal transcribed spacer (ITS) sequences in GenBank are investigated and a new web-based tool with which these sequences can be explored is introduced. All fungal ITS sequences in GenBank were classified as either identified to species level or insufficiently identified and compared using BLAST. The results are made available as a biweekly updated web service that can be queried to retrieve all insufficiently identified sequences (IIS) associated with any fungal genus. The most commonly available annotation items in GenBank are isolation source (55%); country of origin (50%); and specific host (38%). The molecular sampling of fungi shows a bias towards North America, Europe, China, and Japan whereas vast geographical areas remain effectively unexplored. Mycorrhizal and parasitic genera are on average associated with more IIS than are saprophytic taxa. Glomus, Alternaria, and Tomentella are the genera represented by the highest number of insufficiently identified ITS sequences in GenBank. The web service presented (http://andromeda.botany.gu.se/emerencia.html#genus_search) offers new means, particularly for mycorrhizal and plant pathogenic fungi, to examine the IIS in GenBank in a taxon-oriented framework and to explore their metadata in an easily accessible and time-efficient manner. PMID:19121041

Ryberg, Martin; Kristiansson, Erik; Sjökvist, Elisabet; Nilsson, R Henrik

2009-01-01

274

Brittle tail syndrome is an emerging infection in horses caused by a keratinolytic fungus Equicapillimyces hongkongensis gen. nov., sp. nov.  

PubMed

The newly described brittle tail syndrome causes weakening and breakage of the tail hair of horses. Extensive mycological and molecular studies showed that a novel fungus Equicapillimyces hongkongensis gen. nov., sp. nov. is the most likely cause of this syndrome. It is a septate branching hyaline mould which grows optimally at 30°C, requires nicotinic acid but is inhibited by cycloheximide, and specifically infects horse hair. Hyphae fill the core of infected hair shafts with short-necked structures resembling ascomata containing banana-shaped septate ascospore-like structures perforating the hair cortex from within. Compared to asymptomatic horses (n=31), horses with clinical signs of the syndrome (n=22) are significantly more likely to have positive E. hongkongensis gen. nov., sp. nov. smear (6.5% vs. 100%), culture (6.5% vs. 72.7%), and PCR (32.3% vs. 100%, P<0.001 for all). No other potential pathogens were found on bacteriological and mycological culture or PCR (for Trichophyton, Microsporum and Epidermophyton). Genotyping of pure E. hongkongensis gen. nov., sp. nov. isolates and their corresponding direct specimens by PCR and sequencing of the 18S rRNA, ITS1-5.8S-ITS2, 28S rRNA, beta-actin, beta-tubulin, and elongation factor 1 alpha showed that they are all identical but unique, and related distantly to fungi mostly in the class Sordariomycetes and the family Ophiostomataceae. Its geographical distribution, environmental or animal reservoirs are still unknown. Besides the ugly appearance of infected horse tails, this fungus may emerge as another equine pathogen if it affects the skin and hoof of horses. PMID:22014601

Wong, Samson S Y; Ngan, Antonio H Y; Riggs, Christopher M; Teng, Jade L L; Choi, Garnet K Y; Poon, Rosana W S; Hui, Janet J Y; Low, Frank J; Luk, Alez; Yuen, Kwok-Yung

2011-10-01

275

Nematode parasites of Puerto Rican tree frogs, Eleutherodactylus spp: two new species and a proposal of Poekilostrongylus gen. nov. (Trichostrongylidae).  

PubMed

Poekilostrongylus puertoricensis gen.nov., sp.nov. is proposed for nematodes recovered from Eleutherodactylus coqui, in Puerto Rico. The new genus is similar to Oswaldocruzia Travassos, 1917, but lacks longitudinal ridges on the cuticle. Oswaldocruzia lenteixierai Viqueras, 1938, is partially redescribed, and a key to the genera of the Oswaldocruziinae is given. Thelandros (Parathelandros) garciai sp.nov. is described from E. antillensis and E. portoricensis. Strongyloides sp. was found in E. antillensis and Aplectana spp. (females) were recovered from E. locustus, E. richmondi and E. coqui. PMID:1128929

Schmidt, G D; Whittaker, F H

1975-04-01

276

GIDL: a rule based expert system for GenBank Intelligent Data Loading into the Molecular Biodiversity database  

PubMed Central

Background In the scientific biodiversity community, it is increasingly perceived the need to build a bridge between molecular and traditional biodiversity studies. We believe that the information technology could have a preeminent role in integrating the information generated by these studies with the large amount of molecular data we can find in bioinformatics public databases. This work is primarily aimed at building a bioinformatic infrastructure for the integration of public and private biodiversity data through the development of GIDL, an Intelligent Data Loader coupled with the Molecular Biodiversity Database. The system presented here organizes in an ontological way and locally stores the sequence and annotation data contained in the GenBank primary database. Methods The GIDL architecture consists of a relational database and of an intelligent data loader software. The relational database schema is designed to manage biodiversity information (Molecular Biodiversity Database) and it is organized in four areas: MolecularData, Experiment, Collection and Taxonomy. The MolecularData area is inspired to an established standard in Generic Model Organism Databases, the Chado relational schema. The peculiarity of Chado, and also its strength, is the adoption of an ontological schema which makes use of the Sequence Ontology. The Intelligent Data Loader (IDL) component of GIDL is an Extract, Transform and Load software able to parse data, to discover hidden information in the GenBank entries and to populate the Molecular Biodiversity Database. The IDL is composed by three main modules: the Parser, able to parse GenBank flat files; the Reasoner, which automatically builds CLIPS facts mapping the biological knowledge expressed by the Sequence Ontology; the DBFiller, which translates the CLIPS facts into ordered SQL statements used to populate the database. In GIDL Semantic Web technologies have been adopted due to their advantages in data representation, integration and processing. Results and conclusions Entries coming from Virus (814,122), Plant (1,365,360) and Invertebrate (959,065) divisions of GenBank rel.180 have been loaded in the Molecular Biodiversity Database by GIDL. Our system, combining the Sequence Ontology and the Chado schema, allows a more powerful query expressiveness compared with the most commonly used sequence retrieval systems like Entrez or SRS.

2012-01-01

277

Evaluation of the Gen-ProbeChlamydia trachomatis Transcription-Mediated Amplification Assay with Urine Specimens from Women  

Microsoft Academic Search

We evaluated the Gen-ProbeChlamydia trachomatistranscription-mediated amplification (TMA) assay with urinespecimensforthedetectionofC.trachomatisinfectionsinwomen.Thenoveltest,basedontheisothermal amplificationofchlamydialRNA,wascomparedwiththeRocheAmplicorPCRwithurineandcellculturewith endocervical specimens. First-catch urine and endocervical swab specimens were collected from a total of 561 patients, of whom 70 (12.3%) were confirmed to have chlamydial infection. The diagnostic sensitivity and specificity of TMA with urine were 91.4 and 99.6%, respectively, and those of Amplicor PCR were 97.1 and 99.8%,respectively.Byrepeatedanalysisofthespecimenswithdiscrepantresults,thesensitivityofTMAcould

RAFAEL PASTERNACK; PAULI VUORINEN; ANDARI MIETTINEN

278

Telmatocola sphagniphila gen. nov., sp. nov., a novel dendriform planctomycete from northern wetlands.  

PubMed

Members of the phylum Planctomycetes are common inhabitants of northern wetlands. We used barcoded pyrosequencing to survey bacterial diversity in an acidic (pH 4.0) Sphagnum peat sampled from the peat bog Obukhovskoye, European North Russia. A total of 21189 bacterial 16S rRNA gene sequences were obtained, of which 1081 reads (5.1%) belonged to the Planctomycetes. Two-thirds of these sequences affiliated with planctomycete groups for which characterized representatives have not yet been available. Here, we describe two organisms from one of these previously uncultivated planctomycete groups. One isolate, strain OB3, was obtained from the peat sample used in our molecular study, while another strain, SP2(T) (=DSM 23888(T)?=?VKM B-2710(T)), was isolated from the peat bog Staroselsky moss. Both isolates are represented by aerobic, budding, pink-pigmented, non-motile, spherical cells that are arranged in unusual, dendriform-like structures during growth on solid media. These bacteria are moderately acidophilic and mesophilic, capable of growth at pH 4.0-7.0 (optimum pH 5.0-5.5) and at 6-30°C (optimum 20-26°C). The preferred growth substrates are various heteropolysaccharides and sugars, the latter being utilized only if provided in low concentrations (?0.025%). In contrast to other described planctomycetes, strains SP2(T) and OB3 possess weak cellulolytic potential. The major fatty acids are C16:1?5c, C18:1?5c, C16:0, and C18:0. Characteristic lipids are the n-C31 polyunsaturated alkene (9-10 double bonds) and C30:1/C32:1 (?-1) hydroxy fatty acids. The G?+?C content of the DNA is 58.5-59.0?mol%. Strains SP2(T) and OB3 share identical 16S rRNA gene sequences, which exhibit only 86 and 87% similarity to those of Gemmata obscuriglobus and Zavarzinella formosa. Based on the characteristics reported here, we propose to classify these novel planctomycetes as representatives of a novel genus and species, Telmatocola sphagniphila gen. nov., sp. nov. PMID:22529844

Kulichevskaya, Irina S; Serkebaeva, Yulia M; Kim, Yongkyu; Rijpstra, W Irene C; Damsté, Jaap S Sinninghe; Liesack, Werner; Dedysh, Svetlana N

2012-04-17

279

Sphaerochaeta globosa gen. nov., sp. nov. and Sphaerochaeta pleomorpha sp. nov., free-living, spherical spirochaetes.  

PubMed

Free-living bacteria with spherical cells 0.5-2.5 µm in diameter were isolated from freshwater sediment. 16S rRNA gene sequence analysis placed the new isolates within the phylum Spirochaetes ('spirochaetes'). The isolates never displayed a helical morphology or motility. Growth occurred in the presence of 100 mg ampicillin l(-1) in complex and defined mineral salts medium amended with vitamins, yeast extract and monosaccharides, disaccharides or soluble starch as fermentable substrates. Two distinct isolates, designated Buddy(T) and Grapes(T), exhibited doubling times of 21±2 and 15±1 h in glucose-amended medium and grew at 15-37 and 15-30 °C. Optimum growth was observed between 25 and 30 °C and pH 6.5-7.5, with no growth below pH 5 or above pH 10. Hexose and pentose fermentation yielded ethanol, acetate and formate as major end products. Growth was strictly fermentative and anaerobic, but the isolates tolerated brief oxygen exposure. Nitrate, sulfate, thiosulfate and carbon dioxide were not used as electron acceptors, but soluble Fe(III) was reduced to Fe(II) in glucose-amended medium. The DNA G+C base contents of isolates Buddy(T) and Grapes(T) were 45.5-46.4 and 47.0-49.2 mol%, respectively. Phospholipid fatty acid (PLFA) profiles contained large proportions of C(14:0) and C(16:0) straight-chain saturated fatty acids; C(16:1)?7c and C(16:1)?9c dominated the mono-unsaturated PLFAs in isolate Grapes(T), whereas isolate Buddy(T) also possessed C(18:1)?5c, C(18:1)?7c and C(18:1)?9c fatty acids. Branched monoenoic acids accounted for up to 12.4 and 30% of the total PLFA in isolates Grapes(T) and Buddy(T), respectively. Based on their unique morphological features and the phylogenetic distance from their closest relatives, we propose the new genus, Sphaerochaeta gen. nov., to accommodate the new isolates within the novel species Sphaerochaeta globosa sp. nov. (type strain Buddy(T) =DSM 22777(T) =ATCC BAA-1886(T)) and Sphaerochaeta pleomorpha sp. nov. (type strain Grapes(T) =DSM 22778(T) =ATCC BAA-1885(T)). Sphaerochaeta globosa is the type species of the genus. PMID:21398503

Ritalahti, Kirsti M; Justicia-Leon, Shandra D; Cusick, Kathleen D; Ramos-Hernandez, Natalia; Rubin, Michael; Dornbush, Jessica; Löffler, Frank E

2011-03-11

280

Epibacterium ulvae gen. nov., sp. nov., epibiotic bacteria isolated from the surface of a marine alga.  

PubMed

Two Gram-reaction-negative, rod-shaped, motile bacteria, designated strains U82 and U95(T), were isolated from the marine alga Ulva australis collected at Sharks Point, Clovelly, a rocky intertidal zone near Sydney, Australia. Both strains were oxidase- and catalase-positive, formed brown- to black-pigmented colonies and required NaCl for growth. Phylogenetic analysis based on nearly complete 16S rRNA gene sequences revealed that these strains belong to the Roseobacter clade within the Alphaproteobacteria. The 16S rRNA genes of both strains were identical across the sequenced 1326 nt, but showed differences in the intergenic spacer region (ITS) between the 16S and the 23S rRNA genes. At the genomic level the DNA G+C contents of strains U82 and U95(T) were identical (52.6?mol%) and they had a DNA-DNA hybridization value of 83.7%, suggesting that these strains belong to the same species. The closest described phylogenetic neighbour to strains U82 and U95(T) was Thalassobius aestuarii DSM 15283(T) with 95.8% 16S rRNA gene sequence similarity. Other close relatives include further species of the genera Thalassobius and Shimia. Strains U82 and U95(T) were negative for bacteriochlorophyll a production, showed antibacterial activity towards other marine bacteria, were resistant to the antibiotics gentamicin and spectinomycin and were unable to hydrolyse starch or gelatin. The major fatty acids (>1%) were 18?:?1?7c, 16?:?0, 18?:?2, 10?:?0 3-OH, 12?:?0, 20?:?1 2-OH and 18?:?0. The polar lipid pattern indicated the presence of phosphatidylglycerol, phosphatidylcholine, two unidentified aminolipids and four unidentified phospholipids. Both strains produced ubiquinone 10 (Q-10) as the sole respiratory lipoquinone. Based on their phenotypic and phylogenetic characteristics, it is suggested that strains U82 and U95(T) are members of a novel species within a new genus for which the name Epibacterium ulvae gen. nov., sp. nov. is proposed. The type strain of the type species is U95(T) (?=?DSM 24752(T)?=?LMG 26464(T)). PMID:22904216

Penesyan, Anahit; Breider, Sven; Schumann, Peter; Tindall, Brian J; Egan, Suhelen; Brinkhoff, Thorsten

2012-08-17

281

A graph based algorithm for adaptable dynamic airspace configuration for NextGen  

NASA Astrophysics Data System (ADS)

The National Airspace System (NAS) is a complicated large-scale aviation network, consisting of many static sectors wherein each sector is controlled by one or more controllers. The main purpose of the NAS is to enable safe and prompt air travel in the U.S. However, such static configuration of sectors will not be able to handle the continued growth of air travel which is projected to be more than double the current traffic by 2025. Under the initiative of the Next Generation of Air Transportation system (NextGen), the main objective of Adaptable Dynamic Airspace Configuration (ADAC) is that the sectors should change to the changing traffic so as to reduce the controller workload variance with time while increasing the throughput. Change in the resectorization should be such that there is a minimal increase in exchange of air traffic among controllers. The benefit of a new design (improvement in workload balance, etc.) should sufficiently exceed the transition cost, in order to deserve a change. This leads to the analysis of the concept of transition workload which is the cost associated with a transition from one sectorization to another. Given two airspace configurations, a transition workload metric which considers the air traffic as well as the geometry of the airspace is proposed. A solution to reduce this transition workload is also discussed. The algorithm is specifically designed to be implemented for the Dynamic Airspace Configuration (DAC) Algorithm. A graph model which accurately represents the air route structure and air traffic in the NAS is used to formulate the airspace configuration problem. In addition, a multilevel graph partitioning algorithm is developed for Dynamic Airspace Configuration which partitions the graph model of airspace with given user defined constraints and hence provides the user more flexibility and control over various partitions. In terms of air traffic management, vertices represent airports and waypoints. Some of the major (busy) airports need to be given more importance and hence treated separately. Thus the algorithm takes into account the air route structure while finding a balance between sector workloads. The performance of the proposed algorithms and performance metrics is validated with the Enhanced Traffic Management System (ETMS) air traffic data.

Savai, Mehernaz P.

282

A spatiotemporal data model for incorporating time in geographic information systems (GEN-STGIS)  

NASA Astrophysics Data System (ADS)

Temporal Geographic Information Systems (TGIS) is a new technology, which is being developed to work with Geographic Information Systems (GIS) that deal with geographic phenomena that change over time. The capabilities of TGIS depend on the underlying data model. However, a literature review of current spatiotemporal GIS data models has shown that they are not adequate for managing time when representing temporal data. In addition, the majority of these data models have been designed to support the requirements of specific-purpose applications. In an effort to resolve this problem, the related literature has been explored. A comparative investigation of the current spatiotemporal GIS data models has been made to identify their characteristics, advantages and disadvantages, similarities and differences, and to determine why they do not work adequately. A new object-oriented General-purpose Spatiotemporal GIS (GEN-STGIS) data model is proposed here. This model provides better representation, storage and management of data related to geographic phenomena that change over time and overcomes some of the problems detected in the reviewed data models. The proposed data model has four key benefits. First, it provides the capabilities of a standard vector-based GIS embedded in the 2-D Euclidean space. Second, it includes the two temporal dimensions, valid time and transaction time, supported by temporal databases. Third, it inherits, from the object oriented approach, the flexibility, modularity and ability to handle the complexities introduced by spatial and temporal dimensions. Fourth, it improves the geographic query capabilities of current TGIS with the introduction of the concept of bounding box while providing temporal and spatiotemporal query capabilities. The data model is then evaluated in order to assess its strengths and weaknesses as a spatiotemporal GIS data model, and to determine how well the model satisfies the requirements imposed by TGIS applications. The practicality of the data model is demonstrated by the creation of a TGIS example and the partial implementation of the model using the POET Java software for developing the object-oriented database. the object-oriented database.

Narciso, Flor Eugenia

283

Kosmotoga olearia gen. nov., sp. nov., a thermophilic, anaerobic heterotroph isolated from an oil production fluid.  

PubMed

A novel thermophilic, heterotrophic bacterium, strain TBF 19.5.1(T), was isolated from oil production fluid at the Troll B oil platform in the North Sea. Cells of strain TBF 19.5.1(T) were non-motile rods with a sheath-like structure, or toga. The strain was Gram-negative and grew at 20-80 degrees C (optimum 65 degrees C), pH 5.5-8.0 (optimum pH 6.8) and NaCl concentrations of 10-60 g l(-1) (optimum 25-30 g l(-1)). For a member of the order Thermotogales, the novel isolate is capable of unprecedented growth at low temperatures, with an optimal doubling time of 175 min (specific growth rate 0.24 h(-1)) and a final optical density of >1.4 when grown on pyruvate at 37 degrees C. Various carbohydrates, proteinaceous compounds and pyruvate served as growth substrates. Thiosulfate, but not elemental sulfur, enhanced growth of the isolate. Sulfate also enhanced growth, but sulfide was not produced. The strain grew in the presence of up to approximately 15 % oxygen, but only if cysteine was included in the medium. Growth of the isolate was inhibited by acetate, lactate and propionate, while butanol and malate prevented growth. The major fermentation products formed on maltose were hydrogen, carbon dioxide and acetic acid, with traces of ethanol and propionic acid. The G+C content of the genomic DNA was 42.5 mol%. Phylogenetic analyses of the 16S and 23S rRNA gene sequences as well as 29 protein-coding ORFs placed the strain within the bacterial order Thermotogales. Based on the phylogenetic analyses and the possession of a variety of physiological characteristics not previously found in any species of this order, it is proposed that the strain represents a novel species of a new genus within the family Thermotogaceae, order Thermotogales. The name Kosmotoga olearia gen. nov., sp. nov. is proposed. The type strain of Kosmotoga olearia is TBF 19.5.1(T) (=DSM 21960(T) =ATCC BAA-1733(T)). PMID:19643902

Dipippo, Jonathan L; Nesbø, Camilla L; Dahle, Håkon; Doolittle, W Ford; Birkland, Nils-Kåre; Noll, Kenneth M

2009-07-30

284

Telmatocola sphagniphila gen. nov., sp. nov., a Novel Dendriform Planctomycete from Northern Wetlands  

PubMed Central

Members of the phylum Planctomycetes are common inhabitants of northern wetlands. We used barcoded pyrosequencing to survey bacterial diversity in an acidic (pH 4.0) Sphagnum peat sampled from the peat bog Obukhovskoye, European North Russia. A total of 21189 bacterial 16S rRNA gene sequences were obtained, of which 1081 reads (5.1%) belonged to the Planctomycetes. Two-thirds of these sequences affiliated with planctomycete groups for which characterized representatives have not yet been available. Here, we describe two organisms from one of these previously uncultivated planctomycete groups. One isolate, strain OB3, was obtained from the peat sample used in our molecular study, while another strain, SP2T (=DSM 23888T?=?VKM B-2710T), was isolated from the peat bog Staroselsky moss. Both isolates are represented by aerobic, budding, pink-pigmented, non-motile, spherical cells that are arranged in unusual, dendriform-like structures during growth on solid media. These bacteria are moderately acidophilic and mesophilic, capable of growth at pH 4.0–7.0 (optimum pH 5.0–5.5) and at 6–30°C (optimum 20–26°C). The preferred growth substrates are various heteropolysaccharides and sugars, the latter being utilized only if provided in low concentrations (?0.025%). In contrast to other described planctomycetes, strains SP2T and OB3 possess weak cellulolytic potential. The major fatty acids are C16:1?5c, C18:1?5c, C16:0, and C18:0. Characteristic lipids are the n-C31 polyunsaturated alkene (9–10 double bonds) and C30:1/C32:1 (?-1) hydroxy fatty acids. The G?+?C content of the DNA is 58.5–59.0?mol%. Strains SP2T and OB3 share identical 16S rRNA gene sequences, which exhibit only 86 and 87% similarity to those of Gemmata obscuriglobus and Zavarzinella formosa. Based on the characteristics reported here, we propose to classify these novel planctomycetes as representatives of a novel genus and species, Telmatocola sphagniphila gen. nov., sp. nov.

Kulichevskaya, Irina S.; Serkebaeva, Yulia M.; Kim, Yongkyu; Rijpstra, W. Irene C.; Damste, Jaap S. Sinninghe; Liesack, Werner; Dedysh, Svetlana N.

2012-01-01

285

Mongoliitalea lutea gen. nov., sp. nov., an alkaliphilic, halotolerant bacterium isolated from a haloalkaline lake.  

PubMed

Two bacterial isolates from the surface water of a haloalkaline lake on the Mongolia Plateau, strains MIM18(T) and MIM19, were characterized; their morphological, physiological and chemotaxonomic characters, and phylogenetic position based on 16S rRNA gene sequences, were determined. The two strains were alkaliphilic, halotolerant, non-motile, aerobic, Gram-negative, orange-red, rod-shaped and oxidase-positive. Growth was observed in 0-5.5% (w/v) NaCl, with optimum growth at 1%. The temperature range for growth was 0-41 °C, with good growth at 28-37 °C and optimum growth at 30-33 °C. The DNA G+C content was 39.8-41.2 mol%. The strains contained menaquinone MK-7 as the major respiratory quinone and phosphatidylcholine, phosphatidylglycerol and phosphatidylethanolamine as the major polar lipids. Predominant cellular fatty acids were iso-C(15:0) (28.1-29.3%), iso-C(17:0) 3-OH (14.6-18.8%), C(15:1)?6c (5.3-8.6%), C(14:0) 2-OH and/or iso-C(15:0) 2-OH (5.4-6.1%), and iso-C(17:1)?9c and/or C(16:0) 10-methyl (5.0-6.8%). 16S rRNA gene sequence analysis showed that Belliella and Nitritalea of the family Cyclobacteriaceae were the closest related species with sequence similarities of 91.7-92.3% and 88.2%, respectively, with strains of these genera; other members of the Cyclobacteriaceae had sequence similarities lower than 88%. Phylogenetic analysis indicated that the strains formed a deep-rooted lineage distinct from the clades represented by the genera Belliella, Nitritalea, Indibacter, Aquiflexum, Echinicola, Litoribacter, Cyclobacterium and Algoriphagus. Based on the phenotypic and phylogenetic characteristics mentioned above, the two strains are representatives of a single novel species in a new genus; the name Mongoliitalea lutea gen. nov., sp. nov. is proposed, with MIM18(T) (=ACCC 05421(T)=KCTC 23224(T)) as the type strain. PMID:21551330

Yang, C X; Liu, Y P; Bao, Q H; Feng, F Y; Liu, H R; Zhang, X J; Zhao, Y L

2011-05-06

286

Fuchsiella alkaliacetigena gen. nov., sp. nov., an alkaliphilic, lithoautotrophic homoacetogen from a soda lake.  

PubMed

The first alkaliphilic obligately anaerobic hydrogenotrophic homoacetogenic bacterium, strain Z-7100(T), was isolated from sediments of the soda-depositing soda lake Tanatar III (Altay, Russia). Cells were thin, flexible rods, motile, Gram-negative and spore-forming. The organism was an obligate alkaliphile, growing at pH 8.5 to 10.5, with optimum growth at pH 8.8-9.3, and it grew in soda brines containing 1.9-4.7 M total Na(+) (optimum at 2.8-3.3 M). It exhibited an obligate dependence upon sodium carbonate but not upon chloride ions with an NaCl range for growth of 0-14% (w/v) and an optimum at 7.0-8.5% (w/v). The isolate was mesophilic and grew at temperatures from 25 to 45 °C, with an optimum at 40 °C. An H(2)+CO(2) mixture, ethanol, pyruvate and lactate were utilized with the formation of acetate as the sole metabolic product. Carbohydrates and amino acids did not support growth. The isolate had a respiratory type of metabolism, reducing NO3(-), SeO(4)(2-) or anthraquinone-2,6-disulfonate (as electron acceptors with ethanol as an electron donor). It was able to grow chemolithotrophically on H(2)+CO(2) in medium supplemented with a vitamin solution only. The major cellular fatty acids were the saturated fatty acids anteiso-C(15), C(14:0) and C(16:0) and the aldehydes C(16), C(14) and anteiso-C(15). The DNA G+C content of the isolate was 32.0 mol%. 16S rRNA gene sequence analysis showed that strain Z-7100(T) is a member of the order Halanaerobiales and represents a new branch within the family Halobacteroidaceae, clustering with the type strain of Selenihalanaerobacter shriftii (92.9% gene sequence similarity). On the basis of its physiological characteristics and phylogenetic position, the isolate is considered to represent a novel species in a new genus within the family Halobacteroidaceae. The name Fuchsiella alkaliacetigena gen. nov., sp. nov. is proposed. The type strain of the type species is Z-7100(T) (=DSM 24880(T)=VKM B-2667(T)). PMID:21908678

Zhilina, Tatyana N; Zavarzina, Daria G; Panteleeva, Angela N; Osipov, Georgy A; Kostrikina, Nadezhda A; Tourova, Tatyana P; Zavarzin, Georgy A

2011-09-09

287

Naasia aerilata gen. nov., sp. nov., a member of the family Microbacteriaceae isolated from air.  

PubMed

A Gram-positive, aerobic, rod-shaped bacterial strain, 5116S-4(T), was isolated from an air sample collected in Suwon city, Republic of Korea. Phylogenetic analysis based on 16S rRNA gene sequences indicated that this strain was a new member of the family Microbacteriaceae. The sequence similarities of this strain to the members of the family Microbacteriaceae were less than 97 %, with the highest values observed with Cryobacterium mesophilum MSL-15(T) (96.3 %), Cryobacterium roopkundense RuGl7(T) (96.2 %), Labedella gwakjiensis KSW2-17(T) (96.2 %), Cryobacterium luteum Hh15(T) (96.2 %), Cryobacterium psychrophilum DSM 4854(T) (96.2 %), Klugiella xanthotipulae 44C3(T) (96.0 %) and Amnibacterium kyonggiense KSL51201-037(T) (96.0 %). According to the phylogenetic tree, strain 5116S-4(T) formed a cluster with A. kyonggiense KSL51201-037(T), Labedella gwakjiensis KSW2-17(T) and Lysinimonas soli SGM3-12(T) (95.3 % sequence similarity) on the support of high bootstrap values. Cells were motile with single polar flagellum and showed optimum growth at 30 °C and pH 7 without NaCl. Predominant cellular fatty acids were anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. Polar lipids were diphosphatidylglycerol, dimannosyldiacylglycerol, phosphatidylglycerol, one unknown glycolipid, one unknown phospholipid and one unknown lipid. The acyl type of the cell-wall muramic acid was the acetyl type. Peptidoglycan was supposed to be the type B1 with 2,4-diaminobutyric acid on position 3. Strain 5116S-4(T) was clearly distinguishable from the phylogenetically related genera in the family Microbacteriaceae in terms of chemotaxonomic characteristics. On the basis of the chemotaxonomic and phylogenetic characteristics, a novel genus and species are proposed, Naasia aerilata gen. nov., sp. nov. The type strain of Naasia aerilata is 5116S-4(T) ( = KACC 15517(T) = NBRC 108725(T)). PMID:23203625

Weon, Hang-Yeon; Kim, Soo-Jin; Jang, Yun-Hee; Hamada, Moriyuki; Tamura, Tomohiko; Ahn, Jae-Hyung; Suzuki, Ken-ichiro; Kwon, Soon-Wo

2012-11-30

288

Saliterribacillus persicus gen. nov., sp. nov., a moderately halophilic bacterium isolated from a hypersaline lake.  

PubMed

A novel Gram-positive, moderately halophilic bacterium, designated strain X4B(T), was isolated from soil around the hypersaline lake Aran-Bidgol in Iran and characterized taxonomically using a polyphasic approach. Cells of strain X4B(T) were motile rods and formed ellipsoidal endospores at a terminal or subterminal position in swollen sporangia. Strain X4B(T) was a strictly aerobic bacterium, catalase- and oxidase-positive. The strain was able to grow at NaCl concentrations of 0.5-22.5 % (w/v), with optimum growth occurring at 7.5 % (w/v) NaCl. The optimum temperature and pH for growth were 35 °C and pH 7.0. Analysis of 16S rRNA gene sequence revealed that strain X4B(T) is a member of the family Bacillaceae, constituting a novel phyletic lineage within this family. Highest sequence similarities were obtained with the 16S rRNA gene sequences of the type strains of Sediminibacillus albus (96.0 %), Paraliobacillus ryukyuensis (95.9 %), Paraliobacillus quinghaiensis (95.8 %) and Sediminibacillus halophilus (95.7 %), respectively. The DNA G+C content of this novel isolate was 35.2 mol%. The major cellular fatty acids of strain X4B(T) were anteiso-C(15 : 0) and anteiso-C(17 : 0) and its polar lipid pattern consisted of diphosphatidylglycerol, phosphatidylglycerol, two aminolipids, an aminophospholipid and an unknown phospholipid. The isoprenoid quinones were MK-7 (89 %) and MK-6 (11 %). The peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. On the basis of 16S rRNA gene sequence analysis in combination with chemotaxonomic and phenotypic data, strain X4B(T) represents a novel species in a new genus in the family Bacillaceae, order Bacillales for which the name Saliterribacillus persicus gen. nov., sp. nov. is proposed. The type strain of the type species (Saliterribacillus persicus) is X4B(T) ( = IBRC-M 10629(T) = KCTC 13827(T)). PMID:22447700

Amoozegar, Mohammad Ali; Bagheri, Maryam; Didari, Maryam; Shahzedeh Fazeli, Seyed Abolhassan; Schumann, Peter; Sánchez-Porro, Cristina; Ventosa, Antonio

2012-03-23

289

Pseudenhygromyxa salsuginis gen. nov., sp. nov., a myxobacterium isolated from an estuarine marsh.  

PubMed

A myxobacterial strain, designated SYR-2(T), was obtained from a mud sample from an estuarine marsh alongside the Yoshino River, Shikoku, Japan. It had rod-shaped vegetative cells and formed bacteriolytic enlarging colonies or so-called 'swarms' in the agar media. Fruiting-body-like globular to polyhedral cell aggregates and myxospore-like spherical to ellipsoidal cells within them were observed. Those features coincided with the general characteristics of myxobacteria. The strain was mesophilic and strictly aerobic. Growth of SYR-2(T) was observed at 18-40 °C (optimum, 30-35 °C), pH 5.5-8.3 (optimum, pH 7.0-7.5) and with 0.0-2.5?% (w/v) NaCl (optimum, 0.2-1.0?%). Both Mg(2+) and Ca(2+) were essential cations for the growth. The predominant fatty acids were iso-C15?:?0 (43.8?%), iso-C17?:?0 (22.4?%) and iso-C16?:?0 (9.6?%). A C20?:?4 fatty acid [arachidonic acid (4.3?%)], iso-C19?:?0 (1.5?%) and anteiso-acids [ai-C15?:?0 (0.5?%), ai-C17?:?0 (0.3?%)] were also detected. The G+C content of the DNA was 69.7 mol%. The strain contained menaquinone-7 (MK-7) as the major respiratory quinone. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain SYR-2(T) belonged to the suborder Nannocystineae, order Myxococcales in the class Deltaproteobacteria, and the strain was most closely related to two type strains of marine myxobacteria, Enhygromyxa salina SHK-1(T) and Plesiocystis pacifica SIR-1(T), with 96.5?% and 96.0?% similarities, respectively. These characteristics determined in this polyphasic study suggested that strain SYR-2(T) represents a novel species in a new genus of myxobacteria. The name Pseudenhygromyxa salsuginis gen. nov., sp. nov. is proposed to accommodate this isolate, and the type strain of Pseudenhygromyxa salsuginis is SYR-2(T) (?=?NBRC 104351(T)?=?DSM 21377(T)). PMID:22821734

Iizuka, Takashi; Jojima, Yasuko; Hayakawa, Atsushi; Fujii, Takayoshi; Yamanaka, Shigeru; Fudou, Ryosuke

2012-07-20

290

Desmozoon lepeophtherii n. gen., n. sp., (Microsporidia: Enterocytozoonidae) infecting the salmon louse Lepeophtheirus salmonis (Copepoda: Caligidae)  

PubMed Central

Background A microsporidian was previously reported to infect the crustacean parasite, Lepeophtheirus salmonis (Krøyer, 1837) (Copepoda, Caligidae), on farmed Atlantic salmon (Salmo salar L.) in Scotland. The microsporidian was shown to be a novel species with a molecular phylogenetic relationship to Nucleospora (Enterocytozoonidae), but the original report did not assign it to a genus or species. Further studies examined the development of the microsporidian in L. salmonis using electron microscopy and re-evaluated the molecular findings using new sequence data available for the group. Here we report a full description for the microsporidian and assign it to a new genus and species. Results The microsporidian infects subcuticular cells that lie on the innermost region of the epidermal tissue layer beneath the cuticle and along the internal haemocoelic divisions. The mature spores are sub-spherical with a single nucleus and an isofilar polar filament with 5-8 turns in a double coil. The entire development is in direct contact with the host cell cytoplasm and is polysporous. During early merogony, a diplokaryotic nuclear arrangement exists which is absent throughout the rest of the developmental cycle. Large merogonial plasmodia form which divide to form single uninucleate sporonts. Sporogonial plasmodia were not observed; instead, binucleate sporonts divide to form two sporoblasts. Prior to final division, there is a precocious development of the polar filament extrusion apparatus which is associated with large electron lucent inclusions (ELIs). Analyses of DNA sequences reveal that the microsporidian is robustly supported in a clade with other members of the Enterocytozoonidae and confirms a close phylogenetic relationship with Nucleospora. Conclusion The ultrastructural findings of the precocious development of the polar filament and the presence of ELIs are consistent with those of the Enterocytozoonidae. However, the confirmed presence of an early diplokaryotic stage and a merogonial plasmodium that divides to yield uninucleate sporonts instead of transforming into a sporogonial syncitium, are features not currently associated with the family. Yet, analyses of DNA sequence data clearly place the microsporidian within the Enterocytozoonidae. Therefore, due to the novelty of the copepod host, the ultrastructural findings and the robust nature of the phylogenetic analyses, a new genus should be created within the Enterocytozoonide; Desmozoon lepeophtherii n. gen. n. sp. is proposed.

2009-01-01

291

Proteiniphilum acetatigenes gen. nov., sp. nov., from a UASB reactor treating brewery wastewater.  

PubMed

Two proteolytic, strictly anaerobic bacterial strains (TB107(T) and TB6-6) were isolated from the granule sludge of an upflow anaerobic sludge blanket reactor treating brewery wastewater. The strains were Gram-negative, non-spore-forming and motile. Cells were rod-shaped (0.6-0.9x1.9-2.2 microm). Growth of the strains was observed at 20-45 degrees C and pH 6.0-9.7. The strains were proteolytic. Yeast extract, peptone, pyruvate, glycine and l-arginine could be used as carbon and energy sources. Weak growth was also observed with tryptone, l-serine, l-threonine and l-alanine as carbon and energy sources. Both strains did not use any of the tested carbohydrates, alcohols and fatty acids except pyruvate. Acetic acid and NH3 were produced from yeast extract, peptone and l-arginine, and propionic acid was also produced from yeast extract. Pyruvate was converted to acetic acid and CO2. Gelatin was not hydrolysed. Indole and H2S were not produced. The two strains did not grow in medium containing 20 % bile. Addition of strain TB107T to a syntrophic propionate-degrading co-culture accelerated the propionate-degradation rate. The predominant cellular fatty acid was the branched-chain fatty acid anteiso-C(15 : 0) (46.21 %). The genomic DNA G+C contents of strains TB107T and TB6-6 were 46.6 and 48.9 mol%, respectively. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the two strains represent a new phyletic sublineage within the Cytophaga-Flavobacterium-Bacteroides (CFB) group, with <91 % 16S rRNA gene sequence similarity to the closest species with validly published names. On the basis of polyphasic evidence from this study, a new genus and species, Proteiniphilum acetatigenes gen. nov., sp. nov., is proposed, with strain TB107T (=JCM 12891T=AS 1.5024T) as the type strain. PMID:16280479

Chen, Shuangya; Dong, Xiuzhu

2005-11-01

292

Ultrastructure and 18S rDNA phylogeny of Apoikia lindahlii comb. nov. (Chrysophyceae) and its epibiontic protists, Filos agilis gen. et sp. nov. (Bicosoecida) and Nanos amicus gen. et sp. nov. (Bicosoecida).  

PubMed

Three heterotrophic stramenopiles--Apoikia lindahlii comb. nov. (Chrysophyceae), Filos agilis gen. et sp. nov. (Bicosoecida), and Nanos amicus gen. et sp. nov. (Bicosoecida)--were isolated from acidic peat bogs. The biflagellate A. lindahlii forms loose irregular colonies from which swimming cells may detach, and produces extensive mucilaginous material containing bacterial cells. Phylogenetic analyses of small subunit rDNA sequences demonstrated that A. lindahlii branches within the Chrysophyceae. While A. lindahlii is an obligate heterotroph, ultrastructural observations revealed a leukoplast in the perinuclear region. The pico-sized uniflagellates F. agilis and N. amicus were isolated from separate lakes and within the mucilage of A. lindahlii, suggesting their close associations in natural habitats. In SSU rDNA phylogenies, F. agilis and N. amicus were closely related to the bicosoecids Adriamonas, Siluania, Paramonas, and Nerada. While Filos, Nanos, and Siluania are similar in light microscopic features, their SSU rDNA gene sequences differed significantly (>8% differences) and were not monophyletic. Both F. agilis and N. amicus have a cytostome/cytopharynx particle ingestion apparatus. Bacterial cells and material similar to the mucilage of A. lindahlii occurred within the food vacuole of F. agilis and N. amicus. The nature of association between A. lindahlii and its epibiontic bicosoecids is discussed. PMID:20022300

Kim, Eunsoo; Yubuki, Naoji; Leander, Brian S; Graham, Linda E

2010-04-01

293

Psychrophilic sulfate-reducing bacteria isolated from permanently cold arctic marine sediments: description of Desulfofrigus oceanense gen. nov., sp. nov., Desulfofrigus fragile sp. nov., Desulfofaba gelida gen. nov., sp. nov., Desulfotalea psychrophila gen. nov., sp. nov. and Desulfotalea arctica sp. nov.  

PubMed

Five psychrophilic, Gram-negative, sulfate-reducing bacteria were isolated from marine sediments off the coast of Svalbard. All isolates grew at the in situ temperature of -1.7 degrees C. In batch cultures, strain PSv29T had the highest growth rate at 7 degrees C, strains ASv26T and LSv54T had the highest growth rate at 10 degrees C, and strains LSv21T and LSv514T had the highest growth rate at 18 degrees C. The new isolates used the most common fermentation products in marine sediments, such as acetate, propionate, butyrate, lactate and hydrogen, but only strain ASv26T was able to oxidize fatty acids completely to CO2. The new strains had growth optima at neutral pH and marine salt concentration, except for LSv54T which grew fastest with 1% NaCl. Sulfite and thiosulfate were used as electron acceptors by strains ASv26T, PSv29T and LSv54T, and all strains except PSv29T grew with Fe3+ (ferric citrate) as electron acceptor. Chemotaxonomy based on cellular fatty acid patterns and menaquinones showed good agreement with the phylogeny based on 16S rRNA sequences. All strains belonged to the delta subclass of Proteobacteria but had at least 9% evolutionary distance from known sulfate reducers. Due to the phylogenetic and phenotypic differences between the new isolates and their closest relatives, establishment of the new genera Desulfotalea gen. nov., Desulfofaba gen. nov. and Desulfofrigus gen. nov. is proposed, with strain ASv26T as the type strain of the type species Desulfofrigus oceanense sp. nov., LSv21T as the type strain of Desulfofrigus fragile sp. nov., PSv29T as the type strain of the type species Desulfofaba gelida sp. nov., LSv54T as the type strain of the type species Desulfotalea psychrophila sp. nov. and LSv514T as the type strain of Desulfotalea arctica sp. nov. PMID:10555345

Knoblauch, C; Sahm, K; Jørgensen, B B

1999-10-01

294

Anatoliacodium gen. nov. (Halimedaceae, Green algae) from the Ilerdian-Cuisian in the Eski?ehir region (Western Central Turkey)  

NASA Astrophysics Data System (ADS)

A new genus Anatoliacodium (Halimedaceae, Green algae) is described from the Ilerdian-Cuisian shallow-water sediments of Eski?ehir region, central-western Turkey. These sequences consist of limestones, clayey limestones, sandy limestones and claystones. Anatoliacodium gen. nov. is characterized by erected calcareous segments with well differentiated inner structure: prevailing with large medulla of more or less densely set parallel filaments and cortical zone of prevailing horizontal to subhorizontal cortical filaments, once branching and without constriction. It is supposed that poorly and rarely preserved noncalcareous structures on the skeleton surface could be reproductive structures. The type species of the new genus is Anatoliacodium xinanmui gen. nov. sp. nov. A further new species is also described: Anatoliacodium merici gen. nov. sp. nov. Finally Gymnocodium nummuliticum Pfender, 1966 is emended and transferred to the genus Anatoliacodium.

Erdem, Nazire Özgen; Radoicic, Rajka

2009-08-01

295

Chalicogloea cavernicola gen. nov., sp. nov. (Chroococcales, Cyanobacteria), from low-light aerophytic environments: combined molecular, phenotypic and ecological criteria.  

PubMed

This work characterizes a unicellular cyanobacterium with nearly spherical cells and thin-outlined sheaths that divide irregularly, forming small packets immersed in a diffluent mucilaginous layer. It was isolated growing on calcite speleothems and walls in a show cave in Collbató (Barcelona, Spain). Spectral confocal laser and transmission electron microscopy were used to describe the morphology, fine structure and thylakoid arrangement. The pigments identified were phycoerythrin, phycocyanin, allophycocyanin and chlorophyll a. Three-dimensional reconstructions, generated from natural fluorescence z-stacks, revealed a large surface area of nearly flat, arm-like thylakoidal membranes connected to each other and forming a unified structure in a way that, to our knowledge, has never been described before. Phylogenetic analyses using the 16S rRNA gene sequence showed 95% similarity to strain Chroococcus sp. JJCM (GenBank accession no. AM710384). The diacritical phenotypic features do not correspond to any species currently described, and the genetic traits support the strain being classified as the first member of an independent genus in the order Chroococcales and the family Chroococcaceae. Hence, we propose the name Chalicogloea cavernicola gen. nov., sp. nov. under the provisions of the International Code of Nomenclature for Algae, Fungi and Plants. The type strain of Chalicogloea cavernicola is COLL 3(T) (=CCALA 975(T) =CCAP 1424/1(T)). PMID:23178723

Roldán, M; Ramírez, M; del Campo, J; Hernández-Mariné, M; Komárek, J

2012-11-23

296

Lanfrediella amphicirrus gen. nov. sp. nov. Nematotaeniidae (Cestoda: Cyclophyllidea), a tapeworm parasite of Rhinella marina (Linnaeus, 1758) (Amphibia: Bufonidae).  

PubMed

The family Nematotaeniidae, tapeworms commonly found in the small intestines of amphibians and reptiles, includes 27 recognised species distributed among four genera: Bitegmen Jones, Cylindrotaenia Jewell, Distoichometra Dickey and Nematotaenia Lühe. The taxonomy of these cestodes is poorly defined, due in part to the difficulties of observing many anatomical traits. This study presents and describes a new genus and species of nematotaeniid parasite found in cane toads (Rhinella marina) from eastern Brazilian Amazonia. The cestodes were collected during the necropsy of 20 hosts captured in the urban area of Belém, Pará. The specimens were fixed and processed for light microscopy, scanning electron microscopy (SEM) and three-dimensional (3D) reconstruction. Samples were also collected for molecular analyses. The specimens presented a cylindrical body, two testes and paruterine organs. However, they could not be allocated to any of the four existing nematotaeniid genera due to the presence of two each of dorsal compact medullary testes, cirri, cirrus pouches, genital pores, ovaries and vitelline glands per mature segment. Lanfrediella amphicirrus gen. nov. sp. nov. is the first nematotaeniid studied using Historesin analysis, SEM and 3D reconstruction, and it is the second taxon for which molecular data have been deposited in GenBank. PMID:22012220

Melo, Francisco Tiago de Vasconcelos; Giese, Elane Guerreiro; Furtado, Adriano Penha; Soares, Maurílio José; Gonçalves, Evonnildo Costa; Vallinoto, Antonio Carlos Rosário; Santos, Jeannie Nascimento dos

2011-09-01

297

Algivirga pacifica gen. nov., sp. nov., a Novel Agar-Degrading Marine Bacterium of the Family Flammeovirgaceae Isolated from Micronesia.  

PubMed

An aerobic, Gram-negative, coccoid to short rod-shaped and non-flagellated marine bacterial strain S354(T) was isolated from seawater of Micronesia. The strain was capable to degrade agar-forming slight depression into agar plate. Growth occurred at a temperature range of 12-44 °C, a pH range of 5-9, and a salinity range of 1-7 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences suggested that S354(T) belongs to the family Flammeovirgaceae. The novel strain was most closely related to Limibacter armeniacum YM 11-185(T) with similarity of 92.5 %. The DNA G+C content was 43.8 mol%. The major fatty acids (>10 %) were iso-C15:0 and C16:1 ?5c. The predominant isoprenoid quinone was determined to be MK-7. Polar lipid profile of S354(T) consisted of phosphatidylethanolamine, unknown polar lipid, and unknown glycolipids. Based on the phenotypic, phylogenetic, biochemical, and physiological tests conducted in this study, S354(T) is proposed to represent a type strain of a novel genus and species. The 16S rRNA gene sequence of S354(T) is registered in GenBank under the accession number JQ639084. The type of strain Algivirga pacifica gen. nov., sp. nov. is S354(T) (=KCCM 90107(T)=JCM 18326(T)). PMID:23907492

Kim, Jennifer Jooyoun; Kim, Ji Hyung; Kwon, Young-Kyung; Kwon, Kae Kyoung; Yang, Sung-Hyun; Jang, Jiyi; Heo, Soo-Jin; Park, Heung-Sik; Jung, Won-Kyo; Lee, Youngdeuk; Kang, Do-Hyung; Oh, Chulhong

2013-08-02

298

Genome sequence and description of Timonella senegalensis gen. nov., sp. nov., a new member of the suborder Micrococcinae  

PubMed Central

Timonella senegalensis strain JC301T gen. nov., sp. nov. is the type strain of T. senegalensis gen. nov., sp. nov., a new species within the newly proposed genus Timonella. This bacterial strain was isolated from the fecal flora of a healthy Senegalese patient. In this report, we detail the features of this organism, together with the complete genome sequence and annotation. Timonella senegalensis strain JC301T exhibits the highest 16S rRNA similarity (95%) with Sanguibacter marinus, the closest validly published bacterial species. The genome of T. senegalensis strain JC301T is 3,010,102-bp long, with one chromosome and no plasmid. The genome contains 2,721 protein-coding genes and 72 RNA genes, including 5 rRNA genes. The genomic annotation revealed that T. senegalensis strain JC301T possesses the complete complement of enzymes necessary for the de novo biosynthesis of amino acids and vitamins (except for riboflavin and biotin), as well as the enzymes involved in the metabolism of various carbon sources, chaperone genes, and genes involved in the regulation of polyphosphate and glycogen levels.

Mishra, Ajay Kumar; Lagier, Jean-Christophe; Robert, Catherine; Raoult, Didier; Fournier, Pierre-Edouard

2013-01-01

299

search GenBank: interactive orchestration and ad-hoc choreography of Web services in the exploration of the biomedical resources of the National Center For Biotechnology Information  

PubMed Central

Background Due to the growing number of biomedical entries in data repositories of the National Center for Biotechnology Information (NCBI), it is difficult to collect, manage and process all of these entries in one place by third-party software developers without significant investment in hardware and software infrastructure, its maintenance and administration. Web services allow development of software applications that integrate in one place the functionality and processing logic of distributed software components, without integrating the components themselves and without integrating the resources to which they have access. This is achieved by appropriate orchestration or choreography of available Web services and their shared functions. After the successful application of Web services in the business sector, this technology can now be used to build composite software tools that are oriented towards biomedical data processing. Results We have developed a new tool for efficient and dynamic data exploration in GenBank and other NCBI databases. A dedicated search GenBank system makes use of NCBI Web services and a package of Entrez Programming Utilities (eUtils) in order to provide extended searching capabilities in NCBI data repositories. In search GenBank users can use one of the three exploration paths: simple data searching based on the specified user’s query, advanced data searching based on the specified user’s query, and advanced data exploration with the use of macros. search GenBank orchestrates calls of particular tools available through the NCBI Web service providing requested functionality, while users interactively browse selected records in search GenBank and traverse between NCBI databases using available links. On the other hand, by building macros in the advanced data exploration mode, users create choreographies of eUtils calls, which can lead to the automatic discovery of related data in the specified databases. Conclusions search GenBank extends standard capabilities of the NCBI Entrez search engine in querying biomedical databases. The possibility of creating and saving macros in the search GenBank is a unique feature and has a great potential. The potential will further grow in the future with the increasing density of networks of relationships between data stored in particular databases. search GenBank is available for public use at http://sgb.biotools.pl/.

2013-01-01

300

Kilianites gen. nov., Himalayitidae (Ammonitina) nouveau du Berriasien de la région de Cabra (province de Cordoba, SE Espagne): descendance de Protacanthodiscus  

NASA Astrophysics Data System (ADS)

A new ammonite genus of the himalayitids is described for the group of Hoplites bergeroni Kilian, 1889. Kilianites gen. nov. is only known by its macroconchs (M), until now ascribed to Protacanthodiscus, macroconch of Durangites (pars), or/and Neocosmoceras. The relationships with Protacanthodiscus and Neocosmoceras are discussed, taking into account characters of the ontogenesis and stratigraphic position: Kilianites gen. nov., of the Berriasian Euxinus Zone, Jacobi Subzone (= calpionellids B zone) succeeds the Durangites-Protacanthodiscus acme in the Upper Tithonian Durangites Zone (= A2 and A3 calpionellids subzones).

Enay, Raymond; Boughdiri, Mabrouk; Hégarat, Gérard Le

1998-10-01

301

Iranotrichia gen. n., a new genus of Scenopinidae (Diptera) from Iran, with a key to window fly genera of the world  

PubMed Central

Abstract An unusual new genus of Scenopinidae, Iranotrichia gen. n., comprising two newly discovered species (Iranotrichia insolita sp. n. and Iranotrichia nigra sp. n.), is described from Iran. Iranotrichia gen. n. are scenopinine window flies with a habitus reminiscent of certain bee fly genera (Bombyliidae), based on colouration and elongate mouthparts and antennae. The phylogenetic placement of this distinctive new genus is discussed and a dichotomous key to world genera is presented. The genus name Kelseyana nom. n. is proposed to replace Caenoneura Kröber, 1924, which was found to be preoccupied by Thomson (1870: 270) (Hymenoptera) and Kirby (1890: 136) (Odonata).

Winterton, Shaun L.; Gharali, Babak

2011-01-01

302

Exploring Gen Y Responses to an Apparel Brand’s Use of Cause-Related Marketing Does Message Matter When It Comes to Support for the Breast Cancer Cause?  

Microsoft Academic Search

This study explored Gen Y’s responses to cause-related marketing (CRM) in apparel advertising. Data were collected from 349 Gen Y consumers to examine the influence of CRM on attitudes and purchase intentions toward an apparel brand. Attitude toward the brand was predicted by awareness of the apparel brand, perception of CRM, evaluation of the advertisement, involvement in the breast cancer

Karen H. Hyllegard; Jennifer Paff Ogle; Ruoh-Nan Yan; Julianne Attmann

2010-01-01

303

Use of swabs without transport media for the Gen-Probe Group A Strep Direct Test.  

PubMed

For several years we used rayon or Dacron swabs with liquid transport media for collection and transport of throat swab specimens for testing with the Gen-Probe Group A Strep Direct Test (GASDT). A report of favorable results with a Dacron swab without any transport media for GASDT by another laboratory prompted us to compare detection of group A streptococci (GAS) with and without transport media (referred to as "wet" and "dry" swabs, respectively). Phase one of this study used swabs seeded with GAS. Initially, six recent clinical isolates of GAS were inoculated onto wet and dry swabs and stored at room temperature (RT). After 1, 2, and 3 days of storage, colony counting and GASDT were performed with the swabs. The results, expressed as the mean percentage of the results at zero time, were as follows: for GASDT with wet swabs at 1, 2, and 3 days, 62, 51, and 56%, respectively; for GASDT with dry swabs at 1, 2, and 3 days, 105, 80, and 85%, respectively; for colony counts with wet swabs at 1, 2, and 3 days, 52, 26, and 13%, respectively; for colony counts with dry swabs at 1, 2, and 3 days, 10, 0, and 0%, respectively. An additional six strains of GAS were tested in a similar manner, except that extracts of pharyngeal flora (PF) were added to the inocula. The results obtained with extracts of PF were comparable to those obtained with GAS alone. We also compared the performance of GASDT with wet and dry swabs stored at RT and 4 degrees C. Ten strains of GAS were inoculated onto wet and dry swabs, and GASDT was performed each day for 9 days. The GASDT results for swabs on day 9, expressed as the mean percentage of the results obtained at zero time, were as follows: dry swab and 4 degrees C, 59%; wet swab and 4 degrees C, 31%; dry swab and RT, 33%; and wet swab and RT, 19%. In phase two of this study we conducted a clinical evaluation to determine whether the differences observed with seeded specimens would also be evident with patient specimens. We used a single dry Dacron swab paired with a single rayon Bacti-Swab with liquid Stuart transport medium for the clinical evaluation. Specimens were collected from 1,005 outpatients, plated onto a Strep Selective Agar plate, and then tested within 30 min by GASDT. If culture of GAS from the same swab is used to define a true-positive test result, the sensitivities and specificities were as follows: GASDT with wet swabs, 86.2 and 98.5%, respectively; GASDT with dry swabs, 90.7 and 98.1%, respectively. However, the use of culture as the "gold standard" may understate the actual performance characteristics of GASDT, particularly for the dry swabs. In conclusion, for GASDT the use of swabs without transport media may be preferable to the use of swabs with transport media. PMID:15243083

Bourbeau, Paul P; Heiter, Barbara J

2004-07-01

304

Progress reports for Gen IV sodium fast reactor activities FY 2007.  

SciTech Connect

An important goal of the US DOE Sodium Fast Reactor (SFR) program is to develop the technology necessary to increase safety margins in future fast reactor systems. Although no decision has been made yet about who will build the next demonstration fast reactor, it seems likely that the construction team will include a combination of international companies, and the safety design philosophy for the reactor will reflect a consensus of the participating countries. A significant amount of experience in the design and safety analysis of Sodium Fast Reactors (SFR) using oxide fuel has been developed in both Japan and France during last few decades. In the US, the traditional approach to reactor safety is based on the principle of defense-in-depth, which is usually expressed in physical terms as multiple barriers to release of radioactive material (e.g. cladding, reactor vessel, containment building), but it is understood that the 'barriers' may consist of active systems or even procedures. As implemented in a reactor design, defense-in-depth is classed in levels of safety. Level 1 includes measures to specify and build a reliable design with significant safety margins that will perform according to the intentions of the designers. Level 2 consists of additional design measures, usually active systems, to protect against unlikely accidental events that may occur during the life of the plant. Level 3 design measures are intended to protect the public in the event of an extremely unlikely accident not foreseen to occur during the plant's life. All of the design measures that make up the first three levels of safety are within the design basis of the plant. Beyond Level 3, and beyond the normal design basis, there are accidents that are not expected to occur in a whole generation of plants, and it is in this class that severe accidents, i.e. accidents involving core melting, are included. Beyond design basis measures to address severe accidents are usually identified as being for prevention of progression into severe accident conditions (prevention of core melting) or for mitigation of severe accident consequences (mitigation of the impact of core melting to protect public health and safety). Because design measures for severe accident prevention and mitigation are beyond the normal design basis, established regulatory guidelines and codes do not provide explicit identification of the design performance requirements for severe accident accommodation. The treatment of severe accidents is one of the key issues of R&D plans for the Gen IV systems in general, and for the Sodium Fast Reactor (SFR) in particular. Despite the lack of an unambiguous definition of safety approach applicable for severe accidents, there is an emerging consensus on the need for their consideration for the design. The US SFR program and Argonne National Laboratory (ANL) in particular have actively studied the potential scenarios and consequences of Hypothetical Core Disruptive Accidents (HCDA) for SFRs with oxide fuel during the Fast Flux Test Facility (FFTF) and Clinch River Breeder Reactor Plant (CRBRP) programs in the 70s and 80s. Later, the focus of the US SFR safety R&D activities shifted to the prevention of all HCDAs through passive safety features of the SFRs with metal fuel in the Integral Fast Reactor (IFR) program, and the study of severe accident consequences was de-emphasized. The goal of this paper is to provide an overview of the current SFR safety approach and the role of severe accidents in Japan and France, in preparation for an expected and more active collaboration in this area between the US, Japan, and France.

Cahalan, J. E.; Tentner, A. M.; Nuclear Engineering Division

2007-10-04

305

Campanamuta mantonae gen. et. sp. nov., an exceptionally preserved arthropod from the Sirius Passet Fauna (Buen Formation, lower Cambrian, North Greenland)  

Microsoft Academic Search

Specimens of the paneuarthropod Campanamuta mantonae gen. et sp. nov. are described from the lower Cambrian Sirius Passet Fauna of North Greenland. It is one of the most common taxa in the present collections from the Sirius Passet Fauna, being represented by some 1700 specimens (19%) of an estimated total of perhaps 8500 fossils of the collections studied. Unusually, much

Graham E. Budd

2011-01-01

306

Detection of Chlamydia trachomatis in symptomatic and asymptomatic populations with urogenital specimens by AMP CT (Gen-Probe Incorporated) compared to others commercially available amplification assays  

Microsoft Academic Search

The present study was designed to evaluate the sensitivity and specificity of AMP CT (Gen–Probe Incorporated, San Diego, CA, USA) on urogenital specimens taken from symptomatic patients and on first void urine (FVU) specimens from asymptomatic patients. In symptomatic patients, 618 specimens from 140 men (140 urethral swabs and 140 FVU) and 202 women (202 endocervical swabs and 136 FVU)

Bertille de Barbeyrac; Marc Géniaux; Claude Hocké; Michel Dupon; Christiane Bébéar

2000-01-01

307

Seismosaurus halli, gen. et sp. nov., a new sauropod dinosaur from the Morrison Formation (Upper Jurassic\\/Lower Cretaceous) of New Mexico, USA  

Microsoft Academic Search

Seismosaurus halli, gen. et sp. nov. (Sauropoda, Diplodocidae) is a new large sauropod from the Brushy Basin Member of the Morrison Formation (Upper Jurassic\\/Lower Cretaceous) of central New Mexico. The holotype is a partially articulated skeleton consisting to date of approximately 20 caudal vertebrae, five sacral vertebrae, eight dorsal vertebrae, partial pelvis, five chevrons, and ribs. Distinguishing features include the

David D. Gillette

1991-01-01

308

ColorHOR-novel graphical algorithm for fast scan of alpha satellite higher-order repeats and HOR annotation for GenBank sequence of human genome  

Microsoft Academic Search

Motivation: GenBank data are at present lacking alpha satellite higher-order repeat (HOR) annotation. Furthermore, exact HOR con- sensus lengths have not been reported so far. Given the fast growth of sequence databases in the centromeric region, it is of increas- ing interest to have efficient tools for computational identification and analysis of HORs from known sequences. Results: We develop a

Vladimir Paar; Nenad Pavin; Marija Rosandic; Matko Gluncic; Ivan Basar; Robert Pezer; Sonja Durajlija Zinic

2005-01-01

309

Vetuformosa buckleyi n. gen., n. sp. (Ephemeroptera: Baetidae; Vetuformosinae n. subfam.), a new subfamily of mayflies in Early Cretaceous Burmese amber  

Microsoft Academic Search

A new subfamily, genus and species of mayflies, Vetuformosa buckleyi n. gen., n. sp. (Ephemeroptera: Baetidae; Vetuformosinae n. subfam.), are described as the first representative of the family Baetidae from Early Cretaceous Burmese amber. The female fossil is characterised by unusually long antennae, two pairs of gonostyli representing a primitive appendiculate ovipositor, sensory patches on sternites 8, 9 and 10,

George Poinar Jr

2011-01-01

310

Protoresinacarus brevipedis gen. n., sp. n. from Early Cretaceous Burmese amber: the first fossil record of mites of the Family Resinacaridae (Acari: Heterostigmata: Pyemotoidea)  

Microsoft Academic Search

A new genus and species of mites, Protoresinacarus brevipedis gen. n., sp. n. (Acari: Heterostigmata: Pyemotoidea), is described from Early Cretaceous Burmese amber. This represents the first fossil record of a member of the family Resinacaridae. It is represented by 21 phoretic females adjacent to an adult mantidfly (Neuroptera: Mantispidae). This is the first record of phoresy of pyemotid mites

Alexandr A. Khaustov; George Poinar Jr

2011-01-01

311

Prototeius stageri, Gen. et sp. Nov., a New Teiid Lizard from the Upper Cretaceous Marshalltown Formation of New Jersey, with a Preliminary Phylogenetic Revision of the Teiidae  

Microsoft Academic Search

A new fossil teiid lizard from the Upper Cretaceous Marshalltown Formation (Campanian) of Monmouth County, New Jersey is described as Prototeius stageri, gen. et sp. nov. Based on the holotypic dentary and referred specimens, the genus is diagnosed by a strongly differentiated heterodont dentition, five premaxillary teeth, paired frontals with well developed crista cranii, and a broad, low sagittal crest

Robert K. Denton Jr; Robert C. ONeill

1995-01-01

312

Stages in the Development of Choriopsoropts Kenyensis Gen. et Sp. N. (Acari: Sarcoptiformes: Psoroptidae), A Body Mange Mite from Captive African Buffalo, Syncerus Caffer, in Kenya.  

National Technical Information Service (NTIS)

Stages in the life cycle of Choriopsoroptes kenyensis gen. et. sp. n. are described. The stages for both sexes consist of the egg, larva, protonymph, triponymph, and adult, with the last 3 showing sexual dimorphism. The adult male forms an attachment pair...

G. K. Sweatman J. A. Bindernagel J. B. Walker

1971-01-01

313

Film and Language Learning in Victorian Schools: A Study of the 2009 Next Gen Program of the "Melbourne International Film Festival"  

ERIC Educational Resources Information Center

This article investigates the role of film in language education based on a study of the 2009 "Melbourne International Film Festival" (MIFF). It is structured around a literature review and results from surveys of students and teachers who participated in the young people's section of the program, Next Gen. The article argues that film can provide…

Lo Bianco, Hana

2010-01-01

314

CHROMOSOMAL MAPPING OF 12 GENE-ASSOCIATED MARKERS IN CATTLE IDENTIFIES NOVEL REGIONS OF CONSERVED SYNTENY BETWEEN THE HUMAN AND BOVINE GEN0MES  

Technology Transfer Automated Retrieval System (TEKTRAN)

Current gene density on the bovine genetic maps is extremely limited and the resolution of the human-bovine comparative map is insufficient for selection of positional candidate genes controlling many economic traits of interest in dairy cattle. This study describes the chromosomal mapping of 12 gen...

315

Human GEN1 and the SLX4-Associated Nucleases MUS81 and SLX1 Are Essential for the Resolution of Replication-Induced Holliday Junctions.  

PubMed

Holliday junctions (HJs), the DNA intermediates of homologous recombination, need to be faithfully processed in order to preserve genome integrity. In human cells, the BLM helicase complex promotes nonnucleolytic dissolution of double HJs. In vitro, HJs may be nucleolytically processed by MUS81-EME1, GEN1, and SLX4-SLX1. Here, we exploit human SLX4-null cells to examine the requirements for HJ resolution in vivo. Lack of BLM and SLX4 or GEN1 and SLX4 is synthetically lethal in the absence of exogenous DNA damage, and lethality is a consequence of dysfunctional mitosis proceeding in the presence of unprocessed HJs. Thus, GEN1 activity cannot be substituted for the SLX4-associated nucleases, and one of the HJ resolvase activities, either of those associated with SLX4 or with GEN1, is required for cell viability, even in the presence of BLM. In vivo HJ resolution depends on both SLX4-associated MUS81-EME1 and SLX1, suggesting that they are acting in concert in the context of SLX4. PMID:24080495

Garner, Elizabeth; Kim, Yonghwan; Lach, Francis P; Kottemann, Molly C; Smogorzewska, Agata

2013-09-27

316

Taxonomic studies on a new marine ciliate, Apocoleps magnus gen. nov., spec. nov. (Ciliophora, Colepidae), isolated from Qingdao, China  

NASA Astrophysics Data System (ADS)

The morphology and infraciliature of a new marine colepid ciliate, Apocoleps magnus gen. nov., spec. nov., are described based on living observations and silver impregnations. The new genus Apocoleps is characterized by having 8 (vs. 6 in most other related genera) armour tiers, spines at both ends of the cell, 3 adoral organelles and plates with 4 reniform uni-windows. Apocoleps magnus spec. nov. is defined by the following features: body elongated and slightly curved, about 100-120µm× 35-45 µm in vivo; anterior tertiary tier plate with four uni-windows, most secondary and main tier plates with four uni-windows, posterior tertiary tier plate with two uni-windows; left plate margin slightly serrated; on average 23 transverse and 22 longitudinal ciliary rows; one terminal contractile vacuole; marine habitat.

Chen, Xiangrui; Warren, Alan; Song, Weibo

2009-12-01

317

Transfer of Propionibacterium innocuum Pitcher and Collins 1991 to Propioniferax gen. nov. as Propioniferax innocua comb. nov.  

PubMed

16S ribosomal DNA analysis indicates that Propionibacterium innocuum is a phylogenetic neighbor of Luteococcus japonicus and that this pair of organisms branches intermediately between the genus Propionibacterium on the one side and the genera Aeromicrobium and Nocardioides on the other side. Phenotypically, strains of P. innocuum differ from species of Propionibacterium by exhibiting aerobic growth and possessing arabinose in the cell wall, they differ from species of Aeromicrobium and Nocardioides by the formation of propionic acid, and they differ from species of Luteococcus in morphology. Consequently, P. innocuum should not be classified with authentic Propionibacterium species, and the transfer of P. innocuum Pitcher and Collins 1991 to a new genus, Propioniferax, as Propioniferax innocua gen. nov., comb. nov. is proposed. PMID:8068545

Yokota, A; Tamura, T; Takeuchi, M; Weiss, N; Stackebrandt, E

1994-07-01

318

Third-Party Evaluation of Petro Tex Hydrocarbons, LLC, ReGen Lubricating Oil Re-refining Process  

SciTech Connect

This report presents an assessment of market, energy impact, and utility of the PetroTex Hydrocarbons, LLC., ReGen process for re-refining used lubricating oil to produce Group I, II, and III base oils, diesel fuel, and asphalt. PetroTex Hydrocarbons, LLC., has performed extensive pilot scale evaluations, computer simulations, and market studies of this process and is presently evaluating construction of a 23 million gallon per year industrial-scale plant. PetroTex has obtained a 30 acre site in the Texas Industries RailPark in Midlothian Texas. The environmental and civil engineering assessments of the site are completed, and the company has been granted a special use permit from the City of Midlothian and air emissions permits for the Texas Commission on Environmental Quality.

Compere, A L [ORNL; Griffith, William {Bill} L [ORNL

2009-04-01

319

Balneomonas flocculans gen. nov., sp. nov., a new cellulose-producing member of the alpha-2 subclass of Proteobacteria.  

PubMed

A new bacterial strain capable of producing cellulose was isolated from a hot spring. The isolate was Gram-negative, aerobic, and rod-shaped. The optimum temperature for growth was 40-45 degrees C. Methanol, glucose and other common carbohydrates were not utilized as sole growth substrates. Thiosulfate was not oxidized. The G+C content of the DNA was determined to be 64.0 mol%. Comparative 16S rDNA analysis indicated that Bosea thiooxidans and some strains of the genus Methylobacterium were the nearest relatives. The isolate can be distinguished from these relatives by its defectiveness in methanol utilization and thiosulfate oxidation. On the basis of its phenotypic properties and phylogeny, it is proposed that the isolate be designated Balneomonas flocculans gen. nov., sp. nov. The type strain is TFBT (= JCM 11936T, = KCTC 12101T, = IAM 15034T, = ATCC BAA-817T). PMID:15046301

Takeda, Minoru; Suzuki, Ichiro; Koizumi, Jun-Ichi

2004-03-01

320

Pankovaia semitubulata gen. et sp. n. (Microsporidia: Tuzetiidae) from nymphs of mayflies Cloeon dipterum L. (Insecta: Ephemeroptera) in Western Siberia.  

PubMed

The ultrastructure of a new microsporidian, Pankovaia semitubulata gen. et sp. n. (Microsporidia: Tuzetiidae), from the fat body of Cloeon dipterum (L.) (Ephemeroptera: Baetidae) is described. The species is monokaryotic throughout the life cycle, developing in direct contact with the host cell cytoplasm. Sporogonial plasmodium divides into 2-8 sporoblasts. Each sporoblast, then spore, is enclosed in an individual sporophorous vesicle. Fixed and stained spores of the type species P. semitubulata are 3.4 x 1.9microm in size. The polaroplast is bipartite (lamellar and vesicular). The polar filament is isofilar, possessing 6 coils in one row. The following features distinguish the genus Pankovaia from other monokaryotic genera of Tuzetiidae: (a) exospore is composed of multiple irregularly laid tubules with a lengthwise opening, referred to as "semitubules"; (b) episporontal space of sporophorous vesicle (SPV) is devoid of secretory formations; (c) SPV envelope is represented by a thin fragile membrane. PMID:18650073

Simakova, Anastasia V; Tokarev, Yuri S; Issi, Irma V

2008-07-22

321

Tardiphaga robiniae gen. nov., sp. nov., a new genus in the family Bradyrhizobiaceae isolated from Robinia pseudoacacia in Flanders (Belgium).  

PubMed

Gram-negative, rod-shaped bacteria were isolated from Robinia pseudoacacia root nodules. On the basis of the 16S rRNA gene phylogeny, they are closely related to Bradyrhizobium, Rhodopseudomonas and Nitrobacter species (97% sequence similarity), belonging to the class Alphaproteobacteria and family Bradyrhizobiaceae. The results of physiological and biochemical tests together with sequence analysis of housekeeping genes (atpD, dnaK, gyrB, recA and rpoB) allowed differentiation of this group from other validly published Bradyrhizobiaceae genera. NodA, nodC and nifH genes could not be amplified. On the basis of genotypic and phenotypic data, these organisms represent a novel genus and species for which the name Tardiphaga robiniae gen. nov., sp. nov. (LMG 26467(T)=CCUG 61473(T)), is proposed. PMID:22444281

De Meyer, Sofie E; Coorevits, An; Willems, Anne

2012-03-21

322

Guidus n. gen. (Cestoda: Tetraphyllidea), with description of a new species and emendation of the generic diagnosis of Marsupiobothrium.  

PubMed

Guidus n. gen. (Cestoda, Tetraphyllidea) is proposed for 3 cestode species from skates (Bathyraja spp.: Rajiformes, Rajidae). Members of Guidus differ from those of all other phyllobothriid genera in possessing 4 sessile and conspicuously muscular, saclike bothridia; a bothridial aperture toward anterior end of scolex, and perpendicular to scolex axis; aperture surrounded by a continuous sphincter of circular muscles, and 1 marginal accessory sucker. A new species, Guidus argentinense n. sp., is described, the diagnosis of Marsupiobothrium antarcticum is emended, and it is transferred to the new genus along with Marsupiobothrium awii. These species can be easily distinguished from G. argentinense by the presence of lappets in the bothridial margin. In addition, the diagnosis of Marsupiobothrium is emended based on the redescription of the type species, Marsupiobothrium alopias. PMID:17001785

Ivanov, Verónica A

2006-08-01

323

Paraphilometroides nemipteri gen. et sp. n. (Nematoda: Philometridae) from the marine fish Nemipterus peronii (Valenciennes) from Malaysia.  

PubMed

A new nematode species, Paraphilometroides nemipteri sp. n. is described from the female specimens collected from the dorsal fin and operculum of the marine perciforme fish, Nemipterus peronii off Kuala Terengganu coastal waters in Malaysia. It considerably differs from all other species in Philometridae in the structure of the head end (presence of wide dorsal and ventral cephalic cuticular alae supported by special inner transverse muscular formations) and, therefore, a new genus Paraphilometroides gen. n. has been erected to accommodate it. Additional characteristic features of P. nemipteri are the presence of cuticular bosses on the body, eight cephalic papillae in the outer circle and four small papillae in the inner circle, and the absence of caudal protrusions. PMID:2488050

Moravec, F; Shaharom-Harrison, F

1989-01-01

324

Arnoldiellina fluorescens gen. et sp. nov.--a new green autofluorescent foraminifer from the Gulf of Eilat (Israel).  

PubMed

A new monothalamous (single-chambered) soft-walled foraminiferal species, Arnoldiellina fluorescens gen. et sp. nov., was isolated from samples collected in the Gulf of Eilat, Israel. The species is characterized by a small elongate organic theca with a single aperture of allogromiids. It is characterized by the emission of green autofluorescence (GAF) that has so far not been reported from foraminifera. Phylogenetic analysis of a fragment of the 18S rDNA indicates that the species is related to a group of monothalamous foraminiferans classified as clade I. Although the morphology of the new species is very different compared to the other members of this clade, a specific helix in 18S rRNA secondary structure strongly supports this position. PMID:22999053

Apothéloz-Perret-Gentil, Laure; Holzmann, Maria; Pawlowski, Jan

2012-09-19

325

Bryobacter aggregatus gen. nov., sp. nov., a peat-inhabiting, aerobic chemo-organotroph from subdivision 3 of the Acidobacteria.  

PubMed

Bryobacter aggregatus gen. nov., sp. nov. is proposed to accommodate three strains of slowly growing, chemo-organotrophic bacteria isolated from acidic Sphagnum peat bogs. These bacteria were strictly aerobic, Gram-negative, colourless, non-motile coccoids or short rods that multiplied by normal cell division and formed irregularly shaped cell aggregates. Strains MPL3(T), MPL1011 and MOB76 were acidotolerant, mesophilic organisms capable of growth at pH 4.5-7.2 and between 4 and 33 degrees C (optimum growth at pH 5.5-6.5 and 22-28 degrees C). The preferred growth substrates were sugars, some heteropolysaccharides and galacturonic and glucuronic acids, which are released during decomposition of Sphagnum moss. The major fatty acids were iso-C(15 : 0), C(16 : 0) and summed feature 3 (iso-C(15 : 0) 2-OH and/or C(16 : 1)omega7c); the major quinones were MK-9 and MK-10. The DNA G+C content was 55.5-56.5 mol%. Strains MPL3(T), MPL1011 and MOB76 possessed nearly identical 16S rRNA gene sequences and belonged to the phylum Acidobacteria. They represent the first taxonomically characterized members of acidobacterial subdivision 3 and display only 81.7-86.7 % 16S rRNA gene sequence similarity to other members of the Acidobacteria with validly published names. Therefore, strains MPL3(T), MPL1011 and MOB76 are classified as representatives of a novel species in a new genus, for which the name Bryobacter aggregatus gen. nov., sp. nov. is proposed; strain MPL3(T) (=ATCC BAA-1390(T) =DSM 18758(T)) is the type strain of Bryobacter aggregatus. PMID:19651730

Kulichevskaya, Irina S; Suzina, Natalia E; Liesack, Werner; Dedysh, Svetlana N

2009-08-03

326

Enhanced/synthetic vision and head-worn display technologies for terminal maneuvering area NextGen operations  

NASA Astrophysics Data System (ADS)

NASA is researching innovative technologies for the Next Generation Air Transportation System (NextGen) to provide a "Better-Than-Visual" (BTV) capability as adjunct to "Equivalent Visual Operations" (EVO); that is, airport throughputs equivalent to that normally achieved during Visual Flight Rules (VFR) operations rates with equivalent and better safety in all weather and visibility conditions including Instrument Meteorological Conditions (IMC). These new technologies build on proven flight deck systems and leverage synthetic and enhanced vision systems. Two piloted simulation studies were conducted to access the use of a Head-Worn Display (HWD) with head tracking for synthetic and enhanced vision systems concepts. The first experiment evaluated the use a HWD for equivalent visual operations to San Francisco International Airport (airport identifier: KSFO) compared to a visual concept and a head-down display concept. A second experiment evaluated symbology variations under different visibility conditions using a HWD during taxi operations at Chicago O'Hare airport (airport identifier: KORD). Two experiments were conducted, one in a simulated San Francisco airport (KSFO) approach operation and the other, in simulated Chicago O'Hare surface operations, evaluating enhanced/synthetic vision and head-worn display technologies for NextGen operations. While flying a closely-spaced parallel approach to KSFO, pilots rated the HWD, under low-visibility conditions, equivalent to the out-the-window condition, under unlimited visibility, in terms of situational awareness (SA) and mental workload compared to a head-down enhanced vision system. There were no differences between the 3 display concepts in terms of traffic spacing and distance and the pilot decision-making to land or go-around. For the KORD experiment, the visibility condition was not a factor in pilot's rating of clutter effects from symbology. Several concepts for enhanced implementations of an unlimited field-of-regard BTV concept for low-visibility surface operations were determined to be equivalent in pilot ratings of efficacy and usability.

Arthur, Jarvis J., III; Prinzel, Lawrence J., III; Williams, Steven P.; Bailey, Randall E.; Shelton, Kevin J.; Norman, R. Mike

2011-05-01

327

Thiohalorhabdus denitrificans gen. nov., sp. nov., an extremely halophilic, sulfur-oxidizing, deep-lineage gammaproteobacterium from hypersaline habitats.  

PubMed

Seven strains of extremely halophilic and obligately chemolithoautotrophic sulfur-oxidizing bacteria (SOB) were enriched and isolated at 4 M NaCl from sediments of hypersaline inland lakes in south-eastern Siberia and a Mediterranean sea solar saltern. Cells of the novel isolates were spindle-like, long and non-motile rods with a Gram-negative type of cell wall. They were obligately chemolithoautotrophic SOB using thiosulfate and tetrathionate as electron donors and represent the first example of extremely halophilic chemolithoautotrophs that are able to grow anaerobically with nitrate as electron acceptor. The characteristic feature of the group was the production of large amounts of tetrathionate as an intermediate during the oxidation of thiosulfate to sulfate. With thiosulfate, the novel strains grew within the pH range from 6.5 to 8.2 (optimum at pH 7.5-7.8) and at NaCl concentrations from 1.5 to 4.0 M (optimum at 3.0 M). Cells grown at 4 M NaCl accumulated extremely high concentrations of glycine betaine as a compatible solute. The dominant cellular fatty acids were 10MeC(16 : 0) and C(16 : 0). Based on the DNA-DNA relatedness values, the isolates consisted of a single genomic species and had a similar phenotype. Phylogenetic analysis placed the novel bacteria in the class Gammaproteobacteria as an independent lineage with no significant relationship to any other genera in this class. On the basis of phenotypic and genotypic analysis, the group is proposed to represent a new genus, Thiohalorhabdus gen. nov., with Thiohalorhabdus denitrificans gen. nov., sp. nov. as the type species (type strain HL 19(T)=DSM 15699(T)=UNIQEM U223(T)). PMID:19060078

Sorokin, Dimitry Yu; Tourova, Tatjana P; Galinski, Erwin A; Muyzer, Gerard; Kuenen, J Gijs

2008-12-01

328

Crystallization and preliminary X-ray crystallographic study of GenX, a lysyl-tRNA synthetase paralogue from Escherichia coli, in complex with translation elongation factor P.  

PubMed

GenX, a lysyl-tRNA synthetase paralogue from Escherichia coli, was overexpressed in E. coli, purified by three chromatographic steps and cocrystallized with a lysyl adenylate analogue (LysAMS) by the hanging-drop vapour-diffusion method using PEG 4000 as a precipitant. The GenX-LysAMS crystals belonged to the triclinic space group P1, with unit-cell parameters a=54.80, b=69.15, c=94.08 A, alpha=95.47, beta=106.51, gamma=90.46 degrees, and diffracted to 1.9 A resolution. Furthermore, GenX was cocrystallized with translation elongation factor P (EF-P), which is believed to be a putative substrate of GenX, and LysAMS using PEG 4000 and ammonium sulfate as precipitants. The GenX-EF-P-LysAMS crystals belonged to the monoclinic space group P2(1), with unit-cell parameters a=105.93, b=102.96, c=119.94 A, beta=99.4 degrees, and diffracted to 2.5 A resolution. Structure determination of the E. coli GenX-LysAMS and GenX-EF-P-LysAMS complexes by molecular replacement was successful and structure refinements are now in progress. PMID:20823541

Sumida, Tomomi; Yanagisawa, Tatsuo; Ishii, Ryohei; Yokoyama, Shigeyuki

2010-08-28

329

Acidicapsa borealis gen. nov., sp. nov. and Acidicapsa ligni sp. nov., subdivision 1 Acidobacteria from Sphagnum peat and decaying wood.  

PubMed

Two strains of subdivision 1 Acidobacteria, a pink-pigmented bacterium KA1(T) and a colourless isolate WH120(T), were obtained from acidic Sphagnum peat and wood under decay by the white-rot fungus Hyploma fasciculare, respectively. Cells of these isolates were Gram-negative-staining, non-motile, short rods, which were covered by large polysaccharide capsules and occurred singly, in pairs, or in short chains. Strains KA1(T) and WH120(T) were strictly aerobic mesophiles that grew between 10 and 33 °C, with an optimum at 22-28 °C. Both isolates developed under acidic conditions, but strain WH120(T) was more acidophilic (pH growth range 3.5-6.4; optimum, 4.0-4.5) than strain KA1(T) (pH growth range 3.5-7.3; optimum , 5.0-5.5). The preferred growth substrates were sugars. In addition, the wood-derived isolate WH120(T) grew on oxalate, lactate and xylan, while the peat-inhabiting acidobacterium strain KA1(T) utilized galacturonate, glucuronate and pectin. The major fatty acids were iso-C(15:0) and iso-C(17:1)?8c; the cells also contained significant amounts of 13,16-dimethyl octacosanedioic acid. The quinone was MK-8. The DNA G+C contents of strains KA1(T) and WH120(T) were 54.1 and 51.7 mol%, respectively. Strains KA1(T) and WH120(T) displayed 97.8% 16S rRNA gene sequence similarity to each other. The closest recognized relatives were Acidobacterium capsulatum and Telmatobacter bradus (93.4-94.3% 16S rRNA gene sequence similarity). These species differed from strains KA1(T) and WH120(T) by their ability to grow under anoxic conditions, the absence of capsules, presence of cell motility and differing fatty acid composition. Based on these differences, the two new isolates are proposed as representing a novel genus, Acidicapsa gen. nov., and two novel species. Acidicapsa borealis gen. nov., sp. nov. is the type species for the new genus with strain KA1(T) (=DSM 23886(T)=LMG 25897(T)=VKM B-2678(T)) as the type strain. The name Acidicapsa ligni sp. nov. is proposed for strain WH120(T) (=LMG 26244(T)=VKM B-2677(T)=NCCB 100371(T)). PMID:21856984

Kulichevskaya, Irina S; Kostina, Lilia A; Valásková, Vendula; Rijpstra, W Irene C; Damsté, Jaap S Sinninghe; de Boer, Wietse; Dedysh, Svetlana N

2011-08-19

330

[Difficilina cerebratuli gen. et sp. n. (Eugregarinida: Lecudinidae)--a new gregarine species from the nemertean Cerebratulus barentsi (Nemertini: Cerebratulidae)].  

PubMed

A new species of aseptate gregarine, Difficilina cerebratuli gen. et sp. n. (order Eugregarinida Leger, 1900; suborder Aseptata Chakravarty, 1960; family Lecudinidae Kamm, 1922) from the gut of the White Sea nemertean Cerebratulus barentsi Bürger, 1895, has been described. The electron and light microscopic data on trophozoites are presented. Their general morphology resembles the representatives of the genus Lecudina, but the features of the epicyte ultrastructure are different from Lecudina and similar to those of the Lankesteria spp. Taxonomy of the described species is discussed. Certain ultrastructural characters are included in its generic and specific diagnoses. Genus Difficilina gen. n. Type species: Difficilina cerebratuli sp. n. DIAGNOSIS: Characters of the family. Free trophozoites elongated, anterior end rounded, without hooks or exfoliations, not separated from the rest of the body, with well-developed terminal smooth area. The epicytic folds undulating vertically, in cross sections--monomorphic, finger-shaped, with strongly developed cell-coat, with additional electron-dense axial structure ("middle axis") at the tops; number of rippled dense structurtes and apical filaments 3, the furthers are thick and slightly flattened in diameter. Other stages unknown. In testinal parasites of nemerteans. DIFFERENTIAL DIAGNOSIS: The new genus differs from Lecudina by presence of smooth area at the apical pole of the body and the epicyte structure: vertically undulating monomorphic finger-shaped (in cross section) epicytic folds, oligomerization of the rippled dense structures and apical filaments, and development of the "middle axis". It also differs from Lankesteria by the shape of the body, vertical undulation of the folds, and non-tunicate host. Difficilina cerebratuli sp. n. DIAGNOSIS: Characters of the genus. Free trophozoites slightly bent, up to 250 x 70 microm. Anterior end with less granular cytoplasm; with feebly marked apical papilla encircled by the smooth area. Posterior end pointed. The average height of the epicytic folds is 280 nm, thickness--160 nm, average distance between folds is 130 nm. Endoplasm contains a number of accumulations of the fibrillar matter. Nucleus spherical 14-26 microm in diameter, localized in the middle or in the fore third of the body, carries 1-2 karyosomes of various size. Other stages unknown. TYPE SERIES: Microscopical slide with 7 trophozoites (Bouin, Delafield's haematoxylin) is kept in the Zoological museum of the Moscow State University (collection number: Z-2). In addition, two syntypes are observed with TEM and two other syntypes--with SEM. TYPE HOST: Cerebratulus barentsi Bürger, 1895 (Nemertini: Cerebratulidae). LOCATION: Intestine (?). TYPE LOCALITY: White Sea Biological Station of the Moscow State University, Yeremeyevsky Rapid, Velikaya Salma Strait, Kandalaksha Bay, White Sea. PMID:19807039

Simdianov, T G

331

[Sphinctocystis phyllodoces gen. n., sp. n. (Eugregarinida: Lecudinidae)--a new gregarine from Phyllodoce citrina (Polychaeta: Phyllodocidae)].  

PubMed

A new species of aseptate gregarine, Sphinctocystis phyllodoces gen. n., sp. n., from the gut of a polychaete Phyllodoce citrina Malmgren, 1865 from White Sea is described. The electron and light microscopic data on trophozoits are presented. Taxonomy of the described species is discussed. Certain ultrastructural characters are included in generic and specific diagnoses. Order Eugregarinida Leger, 1900; suborder Aseptata Chakravarty, 1960; family Lecudinidae Kamm, 1922. GENUS: Sphinctocystis gen. n. TYPE SPECIES: Sphinctocystis phyllodoces sp. n. DIAGNOSIS: Characters of the family. Free trophozoits elongated, often with several annular constrictions. Anterior end asymmetric, without hooks, not separated from the body, with small apical papilla encircled by smooth area. Epicyte "classical", without additional axial formations at the tops of folds; epicytic folds high, monomorphic in cross sections, finger-shaped, with parallel sidewalls. In the gut of polychaetes. DIFFERENTIAL DIAGNOSIS: The new genus differs from Lecudina by having asymmetric anterior end, developed smooth area around the apical papilla, and monomorphic epicytic folds looking finger-shaped in cross sections. It also differs from Lankesteria by the absence of additional axial formations at the tops of the epicytic folds. It differs from both named genera by presence of annular constrictions on the trophozoit body. Sphinctocystis phyllodoces sp. n. DIAGNOSIS: Characters of the genus. Free trophozoits elongated, large, up to 617 x x 77 um. The average height of epicytic folds 976 nm, thickness 194 nm; there are 6-8 apical filaments and rippled dense structures per fold. Nucleus spherical (ellipsoid after fixation), 24-52 microm along longest axis, localised in anterior third of the body, carries several karyosomes of various size; 25-30 nm thick fibrils (possible fragments of nucleolonema) may be present in karyolymph. Other stages unknown. TYPE SERIES: Microscope preparation with 7 trophozoits, Karacci's haematoxylin stained, is kept in the Zoological museum of the Moscow State University (collection number: Z-1). TYPE HOST: Phyllodoce citrina Malmgren, 1865 (Polychaeta: Phyllodocidae). LOCALISATION: Mid-gut. TYPE LOCALITY: White Sea Biological Station of the Moscow State University, Yeremeyevsky Rapid, Velikaya Salma Strait, Kandalaksha Bay, White Sea. PMID:15493284

Simdianov, T G

332

A new remarkable subterranean beetle of the Rhodopes: Paralovricia gen. n. beroni sp. n. belonging to Lovriciina new subtribe (Coleoptera, Carabidae, Trechinae, Bembidiini)  

PubMed Central

Abstract Paralovricia gen. n. beroni sp. n., belonging to the new subtribe Lovriciina, is described from two caves in the Western Rhodopes (Bulgaria): Kraypatnata peshtera, near Smilyan Village (Smolyan Municipality) and Snezhanka, near Peshtera Town (Peshtera Municipality). Three currently known genera, Lovricia Pretner, 1979, Neolovricia Lakota, Jalži? & Moravec, 2009 and Paralovricia gen. n. represent a monophyletic unit supported by important synapomorphies that allows to propose the establishment of the new subtribe Lovriciina, characterized by the following characters: last maxillary palpomeres very long and narrow, basal angles of pronotum without seta, elytra without discal setae, elytral umbilicate series of nine pores in which the main pores are the 2nd, 6th and 9th, apical recurrent striole absent and mesotibial apex expanded outward. Its systematic position within the subfamily Trechinae (sensu Lorenz 2005) is discussed and Lovriciina is placed near Anillina. Key to the genera of the subtribe is proposed. Distribution data and zoogeographical hypotheses are discussed.

Giachino, Pier Mauro; Gueorguiev, Borislav; Vailati, Dante

2011-01-01

333

Boltimys broomi gen. nov., sp. nov. (Rodentia, Mammalia), nouveau Muridae d'affinité incertaine du Pliocène inférieur d'Afrique du Sud  

NASA Astrophysics Data System (ADS)

Boltimys broomi gen. nov., sp. nov., a Muridae of uncertain affinity in the Early Pliocene of South Africa. Boltimys broomi gen. nov., sp. nov. is reported from the Early Pliocene fauna of Waypoint 160, a fossiliferous locality in the area of Bolt's Farm (Province of Gauteng) near Krugersdorp in South Africa. The occlusal surface of the jugal teeth is characterized by a basin-shaped aspect due to the coalescence of the cusps which make the lobes of the molars. An accessory inner cusp is present on the first and second upper molars. A faint longitudinal crest is present only in the first lower molar. The new rodent is tentatively referred to the subfamily Myocricetodontinae.

Sénégas, Frank; Michaux, Jacques

2000-04-01

334

Non contiguous-finished genome sequence and description of Enorma massiliensis gen. nov., sp. nov., a new member of the Family Coriobacteriaceae  

PubMed Central

Enorma massiliensis strain phIT is the type strain of E. massiliensis gen. nov., sp. nov., the type species of a new genus within the family Coriobacteriaceae, Enorma gen. nov. This strain, whose genome is described here, was isolated from the fecal flora of a 26-year-old woman suffering from morbid obesity. E. massiliensis strain phIT is a Gram-positive, obligately anaerobic bacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,280,571 bp long genome (1 chromosome but no plasmid) exhibits a G+C content of 62.0% and contains 1,901 protein-coding and 51 RNA genes, including 3 rRNA genes.

Mishra, Ajay Kumar; Hugon, Perrine; Lagier, Jean-Christophe; Nguyen, Thi-Tien; Couderc, Carine; Raoult, Didier; Fournier, Pierre-Edouard

2013-01-01

335

Non contiguous-finished genome sequence and description of Dielma fastidiosa gen. nov., sp. nov., a new member of the Family Erysipelotrichaceae  

PubMed Central

Dielma fastidiosa strain JC13T gen. nov., sp. nov. is the type strain of D. fastidiosa gen. nov., sp. nov., the type species of a new genus within the family Erysipelotrichaceae. This strain, whose draft genome is described here, was isolated from the fecal flora of a healthy 16-year-old male Senegalese volunteer. D. fastidiosa is a Gram-negative anaerobic rod. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,574,031 bp long genome comprises a 3,556,241-bp chromosome and a 17,790-bp plasmid. The chromosome contains 3,441 protein-coding and 50 RNA genes, including 3 rRNA genes, whereas the plasmid contains 17 protein-coding genes.

Ramasamy, Dhamodharan; Lagier, Jean-Christophe; Nguyen, Thi Tien; Raoult, Didier; Fournier, Pierre-Edouard

2013-01-01

336

Alcalilimnicola halodurans gen. nov., sp. nov., an alkaliphilic, moderately halophilic and extremely halotolerant bacterium, isolated from sediments of soda-depositing Lake Natron, East Africa Rift Valley  

Microsoft Academic Search

concentrations of 0-28% (w\\/v), with optimal growth at 3-8% (w\\/v) NaCl. The bacterium preferentially metabolized volatile fatty acids and required vitamins for growth. The name Alcalilimnicola halodurans gen. nov., sp. nov. is proposed for the novel isolate, placed in the c-Proteobacteria within the family Ectothiorhodospiraceae on the basis of analysis of the 16S rDNA sequence, polar lipids, fatty acids and

Michail M. Yakimov; Laura Giuliano; Tatiana N. Chernikova; Gabriella Gentile; Wolf-Rainer Abraham; Heinrich Lu; Kenneth N. Timmis; Peter N. Golyshin

337

Neotropical monogenea. 13. Rhinonastes pseuodocapsaloideum n. gen., n. sp. (Dactylogyridae, Ancyrocephalinae), a nasal parasite of curimatã, Prochilodus nigricans Agassiz (Cypriniformes, Prochilodontidae), in Brazil.  

PubMed

Rhinonastes pseudocapsaloideum n. sp. (Dactylogyridae, Ancyrocephalinae) is described from the nasal cavity of Prochilodus nigricans Agassiz (Cypriniformes, Prochilodontidae) in Brazil. Rhinonastes n. gen. is proposed for species possessing a dextroventral genital pore, a bilobed testis, a ventral C-shaped ovary lying between the 2 testicular lobes, and a disc-shaped haptor armed with a ventral anchor-bar complex and 14 hooks. PMID:3397831

Kritsky, D C; Thatcher, V E; Boeger, W A

1988-08-01

338

Evaluation of Performance of the Gen-Probe Human Immunodeficiency Virus Type 1 Viral Load Assay Using Primary Subtype A, C, and D Isolates from Kenya  

PubMed Central

Accurate and sensitive quantification of human immunodeficiency virus type 1 (HIV-1) RNA has been invaluable as a marker for disease prognosis and for clinical monitoring of HIV-1 disease. The first generation of commercially available HIV-1 RNA tests were optimized to detect the predominant HIV-1 subtype found in North America and Europe, subtype B. However, these tests are frequently suboptimal in detecting HIV-1 genetic forms or subtypes found in other parts of the world. The goal of the present study was to evaluate the performance of a new viral load assay with non-subtype B viruses. A transcription-mediated amplification method for detection and quantitation of diverse HIV-1 subtypes, called the Gen-Probe HIV-1 viral load assay, is under development. In this study we examined the performance of the Gen-Probe HIV-1 viral load assay relative to that of the commonly used commercial HIV-1 RNA assays using a panel of primary isolates from Kenya. For comparison, we included several subtype B cloned viruses, and we quantified each virus using an in-house quantitative-competitive reverse transcriptase PCR (QC-RT-PCR) method and gagp24 antigen capture. The Gen-Probe HIV-1 viral load assay and a version of the Roche AMPLICOR HIV-1 MONITOR test (version 1.5) that was designed to detect a broader range of subtypes were both sensitive for the quantification of Kenyan primary isolates, which represented subtype A, C, and D viruses. The Gen-Probe HIV-1 viral load assay was more sensitive for the majority of viruses than the Roche AMPLICOR HIV-1 MONITOR test version 1.0, the Bayer Quantiplex HIV RNA 3.0 assay, or a QC-RT-PCR method in use in our laboratory, suggesting that it provides a useful method for quantifying HIV-1 RNAs from diverse parts of the world, including Africa.

Emery, Sandra; Bodrug, Sharon; Richardson, Barbra A.; Giachetti, Cristina; Bott, Martha A.; Panteleeff, Dana; Jagodzinski, Linda L.; Michael, Nelson L.; Nduati, Ruth; Bwayo, Job; Kreiss, Joan K.; Overbaugh, Julie

2000-01-01

339

A Passive UHF RFID Transponder for EPC Gen 2 with -14dBm Sensitivity in 0.13?m CMOS  

Microsoft Academic Search

A passive RFID transponder conforming to the EPC Gen 2 standard is presented, including an RF and analog front-end, EEPROM, and a digital processing core and features a unique RF sampled analog random number generator to support the required anti-collision protocol. Fabricated in 0.13mum CMOS, the 0.55mm2 IC functions at a sensitivity of -14dBm using an 860-to-960MHz carrier at 40-to-160kb\\/s

Ray Barnett; Ganesh Balachandran; Steve Lazar; Brad Kramer; George Konnail; Suribhotla Rajasekhar; Vladimir Drobny

2007-01-01

340

Petrified plants from the cretaceous of the Kwanto mountains, central Japan. III. A polyxylic cycadean trunk, Sanchucycas gigantea gen. et sp. nov  

Microsoft Academic Search

Sanchucycas gigantea gen. et sp. nov. is a fossil cycadophyte trunk from the Lower Cretaceous (Late Barremian—Early Aptian) Sebayashi Formation\\u000a of the Sanchu area, Gunma Prefecture. It has polycyclic vascular bundles, pitted tracheids, uni- to hexaseriate rays, one\\u000a or two large cross field pits, and mucilage sacs.Sanchucycas is most closely comparable withCycas andEncephalartos among living members of the Cycadales, but

Harufumi Nishida; Makoto Nishida; Kuniyuki Tanaka

1991-01-01

341

A new genus of oak gallwasp, Coffeikokkos Pujade-Villar & Melika, gen. n., with a description of a new species from Costa Rica (Hymenoptera, Cynipidae)  

PubMed Central

Abstract A new genus of oak gallwasp, Coffeikokkos Pujade-Villar & Melika, gen. n., is described from Costa Rica. Diagnostic characters and generic limits of the new genus are discussed in detail. The new genus includes Coffeikokkos copeyensis Pujade-Villar & Melika, sp. n., which induces galls on stems of Quercus bumelioides, an endemic oak to Costa Rica, Honduras and Panama. The new species and galls are described and illustrated.

Pujade-Villar, Juli; Hanson, Paul; Melika, George

2012-01-01

342

Ramlibacter tataouinensis gen. nov., sp. nov., and Ramlibacter henchirensis sp. nov., cyst-producing bacteria isolated from subdesert soil in Tunisia  

Microsoft Academic Search

Ramlibacter gen. nov. is proposed for two aerobic, chemo-organotrophic, cyst-producing soil bacterial strains. These bacteria are Gram-negative, non-flagellated rods or cysts, isolated from subdesert soil in Tataouine, Tunisia. Phylogenetic analyses of the rrs sequences of the two strains showed that they do not constitute a robust clade at the genus level with any previously described bacteria and that they are

Thierry Heulin; Mohamed Barakat; Richard Christen; Maurice Lesourd; Laurent Sutra; Gilles De Luca; Wafa Achouak

2003-01-01

343

Formate-Dependent Growth and Homoacetogenic Fermentation by a Bacterium from Human Feces: Description of Bryantella formatexigens gen. nov., sp. nov.  

PubMed Central

Formate stimulates growth of a new bacterium from human feces. With high formate, it ferments glucose to acetate via the Wood-Ljungdahl pathway. The original isolate fermented vegetable cellulose and carboxymethylcellulose, but it lost this ability after storage at ?76°C. 16S rRNA gene sequencing identifies it as a distinct line within the Clostridium coccoides supra-generic rRNA grouping. We propose naming it Bryantella formatexigens gen. nov., sp. nov.

Wolin, Meyer J.; Miller, Terry L.; Collins, Matthew D.; Lawson, Paul A.

2003-01-01

344

Polymorphisms in the Nonmuscle Myosin Heavy Chain 9 Gene (MYH9) Are Associated with Albuminuria in Hypertensive African Americans: The HyperGEN Study  

Microsoft Academic Search

Background:MYH9 is a podocyte-expressed gene encoding nonmuscle myosin IIA that is associated with idiopathic and human immunodeficiency virus-associated focal segmental glomerulosclerosis (FSGS) and hypertensive end-stage renal disease in African Americans. Methods: Four single nucleotide polymorphisms comprising the major MYH9 E1 risk haplotype were tested for association with estimated glomerular filtration rate (eGFR) and urine albumin:creatinine ratio (ACR) in 2,903 HyperGEN

Barry I. Freedman; Jeffrey B. Kopp; Cheryl A. Winkler; George W. Nelson; D. C. Rao; John H. Eckfeldt; Mark F. Leppert; Pamela J. Hicks; Jasmin Divers; Carl D. Langefeld; Steven C. Hunt

2009-01-01

345

[The impact of gen polymorphism of subunits of receptors of thrombocytes GP IIb/IIIa on variation of indicators of thrombocyte hemostasis in obstetrics practice].  

PubMed

The article presents the results of study of the impact of gen polymorphism of subunits of receptors of thrombocytes GP Ilb/IIIa on variation of quantitative, functional and morphometric parameters of thrombocytes in 408 puerperae. The heterozygous variant of mutation was established in women with physiologically progress of pregnancy and delivery and in women with clinical manifestations of thrombophilia. The homozygous variant was established only in women with thrombophilia. The relationship is established between the presence of hetero- and homozygous mutations of gen of subunits of receptors of thrombocytes GP IIb/IIIa and inclination to hypercoagulation. This relationship manifests itself in increasing of degree of thrombocytes aggregation with all inductors and as well as in increasing of functional activity and appearance of young active cells, according morphometric analysis data. The application of computer morphometry of thrombocytes in the study made it possible to ascertain the activization of thrombocyte component of hemostasis in healthy women and availability of heterozygous mutation of gen of subunits of receptors of thrombocytes GP IIb/IIIa (PlA1/PlA2). PMID:22624463

Bondar', T P; Muratova, A Iu

2012-02-01

346

Comparison of the Agilent, ROMA/NimbleGen and Illumina platforms for classification of copy number alterations in human breast tumors  

PubMed Central

Background Microarray Comparative Genomic Hybridization (array CGH) provides a means to examine DNA copy number aberrations. Various platforms, brands and underlying technologies are available, facing the user with many choices regarding platform sensitivity and number, localization, and density distribution of probes. Results We evaluate three different platforms presenting different nature and arrangement of the probes: The Agilent Human Genome CGH Microarray 44 k, the ROMA/NimbleGen Representational Oligonucleotide Microarray 82 k, and the Illumina Human-1 Genotyping 109 k BeadChip, with Agilent being gene oriented, ROMA/NimbleGen being genome oriented, and Illumina being genotyping oriented. We investigated copy number changes in 20 human breast tumor samples representing different gene expression subclasses, using a suite of graphical and statistical methods designed to work across platforms. Despite substantial differences in the composition and spatial distribution of probes, the comparison revealed high overall concordance. Notably however, some short amplifications and deletions of potential biological importance were not detected by all platforms. Both correlation and cluster analysis indicate a somewhat higher similarity between ROMA/NimbleGen and Illumina than between Agilent and the other two platforms. The programs developed for the analysis are available from . Conclusion We conclude that platforms based on different technology principles reveal similar aberration patterns, although we observed some unique amplification or deletion peaks at various locations, only detected by one of the platforms. The correct platform choice for a particular study is dependent on whether the appointed research intention is gene, genome, or genotype oriented.

Baumbusch, LO; Aar?e, J; Johansen, FE; Hicks, J; Sun, H; Bruhn, L; Gunderson, K; Naume, B; Kristensen, VN; Liest?l, K; B?rresen-Dale, A-L; Lingjaerde, OC

2008-01-01

347

Cipactlichthys scutatus, gen. nov., sp. nov. a New Halecomorph (Neopterygii, Holostei) from the Lower Cretaceous Tlayua Formation of Mexico  

PubMed Central

Based on specimens from the Lower Cretaceous Tlayua Formation of Mexico, we describe a new genus and species of Halecomorphi, Cipactlichthysscutatus gen. et sp. nov, which exhibits several diagnostic characters such as the dermal bones and the scales with ganoin and highly ornamented by numerous tubercles and ridges; parietal slightly longer than wide with approximately the same length as the frontal; jaws extending far, below the posterior orbital margin, reaching the posterior third of the postorbital plate; maxilla with a convexly rounded posterior margin; pectoral fin margins slightly convex; first ray of pectoral fin very long, reaching the posterior edge of the pelvic fin; about 37 preural vertebrae and 7 Ural centra; a series of hypertrophied scales just posterior to the cleithrum; arrangement of flank scales with two rows of deep scales; a series of dorsal and ventral scutes forming the dorsal and ventral midline, between the dorsal and anal fins and the caudal fin. A phylogenetic analysis including two outgroups and eleven neopterygians confirmed the monophyly of the Holostei as well as the monophyly of the Halecomorphi, although this last clade is weakly supported. Cipactlichthysscutatus was hypothesised as the sister-group of the (Ionoscopiformes + Amiiformes).

Brito, Paulo M.; Alvarado-Ortega, Jesus

2013-01-01

348

The ultramicrobacterium "Elusimicrobium minutum" gen. nov., sp. nov., the first cultivated representative of the termite group 1 phylum.  

PubMed

Insect intestinal tracts harbor several novel, deep-rooting clades of as-yet-uncultivated bacteria whose biology is typically completely unknown. Here, we report the isolation of the first representative of the termite group 1 (TG1) phylum from sterile-filtered gut homogenates of a humivorous scarab beetle larva. Strain Pei191(T) is a mesophilic, obligately anaerobic ultramicrobacterium with a gram-negative cell envelope. Cells are typically rod shaped, but cultures are pleomorphic in all growth phases (0.3 to 2.5 microm long and 0.17 to 0.3 microm wide). The isolate grows heterotrophically on sugars and ferments D-galactose, D-glucose, D-fructose, D-glucosamine, and N-acetyl-D-glucosamine to acetate, ethanol, hydrogen, and alanine as major products but only if amino acids are present in the medium. PCR-based screening and comparative 16S rRNA gene sequence analysis revealed that strain Pei191(T) belongs to the "intestinal cluster," a lineage of hitherto uncultivated bacteria present in arthropod and mammalian gut systems. It is only distantly related to the previously described so-called "endomicrobia" lineage, which comprises mainly uncultivated endosymbionts of termite gut flagellates. We propose the name "Elusimicrobium minutum" gen. nov., sp. nov. (type strain, Pei191(T) = ATCC BAA-1559(T) = JCM 14958(T)) for the first isolate of this deep-branching lineage and the name "Elusimicrobia" phyl. nov. for the former TG1 phylum. PMID:19270135

Geissinger, Oliver; Herlemann, Daniel P R; Mörschel, Erhard; Maier, Uwe G; Brune, Andreas

2009-03-06

349

Neotropical Monogenoidea. 40. Protorhinoxenus prochilodi gen. n., sp. n. (Monogenoidea: Ancyrocephalinae), parasite of prochilodus lineatus (Characiformes: Prochilodontidae) from south Brazil.  

PubMed

The monotypic Protorhinoxenus gen. n. is proposed to accommodate a species with the following characteristics: 1) tubular sclerotised vagina, 2) vaginal pore dextrolateral, 3) ventral and dorsal anchors with undifferentiated elongate shaft and base (representing approximately 2/3 of the length of anchor), and 4) superficial and deep roots of ventral and dorsal anchors lacking. Protorhinoxenus prochilodi sp. n. is described from the gills of Prochilodus lineatus (Valenciennes) of the Represa Capivari-Cachoeira, Municipality of Campina Grande do Sul, metropolitan area of Curitiba, Paraná. Specimens of other probable new species of Protorhinoxenus are reported from Prochilodus lineatus of the Rio Paranapanema, Municipality of Salto Grande, São Paulo; Hoplias spp. of the Rio Dois de Fevereiro, Municipality of Antonina, Paraná, and the Rio Piraquara, metropolitan area of Curitiba, Parana; Leporinus elongatus Valenciennes of the Rio Tibagi, Municipality of Jataizinho, Parana; and Schizodon fasciatum Agassiz of the Rio Solimões, island of Marchantaria, near Manaus, Amazonas. Protorhinoxenus appears to be a sister group of Rhinoxenus Kritsky, Boeger et Thatcher, 1988 based on the following apparent synapomorphies: 1) ventral and dorsal anchors lacking superficial and deep roots, 2) ventral and dorsal anchors with elongate shaft, and 3) male copulatory organ with counterclockwise rings. PMID:11993549

Domingues, Marcus V; Boege, Walter A

2002-01-01

350

Phylogenetic analysis identifies the 'megabacterium' of birds as a novel anamorphic ascomycetous yeast, Macrorhabdus ornithogaster gen. nov., sp. nov.  

PubMed

An organism commonly referred to as 'megabacterium' colonizes the gastric isthmus of many species of birds. It is weakly gram-positive and periodic acid-Schiff-positive and stains with silver stains. Previous studies have shown that it has a nucleus and a cell wall similar to those seen in fungi. Calcofluor white M2R staining suggests that the cell wall contains chitin, a eukaryote-specific substance, and rRNA in situ hybridization demonstrates that it is a eukaryote. To characterize this organism phylogenetically, DNA was extracted from purified cells. rDNA was readily amplified by PCR with pan-fungal DNA primer sets and primer sets derived from the newly determined sequence, but not with bacteria-specific primer sets. Specific primer sets amplified rDNA from isthmus scrapings from an infected bird, but not from a non-infected bird or other control DNA. The sequence was confirmed to derive from the purified organism by in situ rRNA hybridization using a specific probe. Phylogenetic analysis of sequences of the 18S rDNA and domain D1/D2 of 26S rDNA showed the organism to be a previously undescribed anamorphic ascomycetous yeast representing a new genus. The name Macrorhabdus ornithogaster gen. nov., sp. nov. is proposed for this organism. The type material is CBS 9251T (= NRRL Y-27487T). PMID:12892150

Tomaszewski, Elizabeth K; Logan, Kathleen S; Snowden, Karen F; Kurtzman, Cletus P; Phalen, David N

2003-07-01

351

Rubritalea marina gen. nov., sp. nov., a marine representative of the phylum 'Verrucomicrobia', isolated from a sponge (Porifera).  

PubMed

A marine bacterium, strain Pol012(T), was isolated from the Mediterranean sponge Axinella polypoides and subsequently characterized as belonging to subphylum 1 of the phylum 'Verrucomicrobia'. Strain Pol012(T) was non-motile, Gram-negative, coccoid or rod-shaped and red in colour. The menaquinones MK-8 and MK-9 were detected. The G+C content of the genomic DNA was 50.9 mol%. Growth was possible at temperatures between 8 and 30 degrees C and at pH values between 6.8 and 8.2. The closest cultured relative of strain Pol012(T) was Akkermansia muciniphila (83 % sequence similarity), while the closest environmental 16S rRNA gene sequence was the marine clone Arctic96BD-2 (95 % sequence similarity). Strain Pol012(T) is the first marine pure-culture representative of 'Verrucomicrobia' subphylum 1 and represents a novel genus and species, for which the name Rubritalea marina gen. nov., sp. nov. is proposed. The type strain is Pol012(T) (=DSM 177716(T)=CIP 108984(T)). PMID:16957108

Scheuermayer, Matthias; Gulder, Tobias A M; Bringmann, Gerhard; Hentschel, Ute

2006-09-01

352

Desulfohalophilus alkaliarsenatis gen. nov., sp. nov., an extremely halophilic sulfate- and arsenate-respiring bacterium from Searles Lake, California  

USGS Publications Warehouse

A haloalkaliphilic sulfate-respiring bacterium, strain SLSR-1, was isolated from a lactate-fed stable enrichment culture originally obtained from the extreme environment of Searles Lake, California. The isolate proved capable of growth via sulfate-reduction over a broad range of salinities (125–330 g/L), although growth was slowest at salt-saturation. Strain SLSR-1 was also capable of growth via dissimilatory arsenate-reduction and displayed an even broader range of salinity tolerance (50–330 g/L) when grown under these conditions. Strain SLSR-1 could also grow via dissimilatory nitrate reduction to ammonia. Growth experiments in the presence of high borate concentrations indicated a greater sensitivity of sulfate-reduction than arsenate-respiration to this naturally abundant anion in Searles Lake. Strain SLSR-1 contained genes involved in both sulfate-reduction (dsrAB) and arsenate respiration (arrA). Amplicons of 16S rRNA gene sequences obtained from DNA extracted from Searles Lake sediment revealed the presence of close relatives of strain SLSR-1 as part of the flora of this ecosystem despite the fact that sulfate-reduction activity could not be detected in situ. We conclude that strain SLSR-1 can only achieve growth via arsenate-reduction under the current chemical conditions prevalent at Searles Lake. Strain SLSR-1 is a deltaproteobacterium in the family Desulfohalobiacea of anaerobic, haloalkaliphilic bacteria, for which we propose the name Desulfohalophilus alkaliarsenatis gen. nov., sp. nov.

Blum, Jodi Switzer; Kulp, Thomas R.; Han, Sukkyun; Lanoil, Brian; Saltikov, Chad W.; Stolz, John F.; Miller, Laurence G.; Oremland, Ronald S.

2012-01-01

353

Schmidingerothrix extraordinaria nov. gen., nov. spec., a secondarily oligomerized hypotrich (Ciliophora, Hypotricha, Schmidingerotrichidae nov. fam.) from hypersaline soils of Africa  

PubMed Central

Schmidingerothrix extraordinaria nov. gen., nov. spec. was discovered in hypersaline soils from Namibia and Egypt. Its morphology and ontogenesis were studied with standard methods. Schmidingerothrix extraordinaria is a highly flexible, slender hypotrich with an average size of 90 × 15 ?m. Likely, it prefers a salinity around 100‰ and feeds mainly on bacteria. Schmidingerothrix is extraordinary in having a frayed buccal lip, three-rowed adoral membranelles, only one frontal cirrus, a distinct gap between frontal and ventral adoral membranelles, and a miniaturized first frontal membranelle, while a paroral membrane, dorsal bristle rows, and buccal, transverse, and caudal cirri are absent. The ontogenesis is simple: the opisthe oral apparatus and frontoventral ciliature originate de novo, while parental structures are involved in the development of the ciliature of the proter. This special organization is used to define a new family, the Schmidingerotrichidae, which is likely related to the Cladotrichidae. Schmidingerothrix extraordinaria is very likely a secondarily oligomerized hypotrich, and the reduction occurred possibly very long ago because no traces of the ancestral ciliature remained in the ontogenetic processes. Possibly, the simple ciliature is an adaptation to highly saline habitats, where competition is low and bacterial food abundant.

Foissner, Wilhelm

2012-01-01

354

Salinarimonas rosea gen. nov., sp. nov., a new member of the alpha-2 subgroup of the Proteobacteria.  

PubMed

A Gram-negative, rod-shaped, facultatively anaerobic, halotolerant bacterial strain, designated YIM YD3(T), was isolated from a salt mine in Yunnan, south-west China. The taxonomy of strain YIM YD3(T) was investigated by a polyphasic approach. Strain YIM YD3(T) was motile, formed pink colonies and was positive for catalase and oxidase activities. Q-10 was the predominant respiratory ubiquinone. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylcholine and two unknown phospholipids. The major fatty acids (>10 % of total fatty acids) were C(18 : 1)omega7c, C(18 : 1)omega9c, C(16 : 0) and C(19 : 0) cyclo omega8c. The DNA G+C content was 71.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed that the isolate formed a distinct line within a clade containing the genera Balneimonas, Bosea, Chelatococcus and Microvirga in the order Rhizobiales, with highest levels of 16S RNA gene sequence similarity to the type strain of Balneimonas flocculans (93.5 %). On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain YIM YD3(T) represents a novel species in a new genus, for which the name Salinarimonas rosea gen. nov., sp. nov. is proposed, with strain YIM YD3(T) (=KCTC 22346(T)=CCTCC AA208038(T)) as the type strain. PMID:19648350

Liu, Ji-Hui; Wang, Yong-Xia; Zhang, Xiao-Xia; Wang, Zhi-Gang; Chen, Yi-Guang; Wen, Meng-Liang; Xu, Li-Hua; Peng, Qian; Cui, Xiao-Long

2009-07-31

355

Aquitalea magnusonii gen. nov., sp. nov., a novel Gram-negative bacterium isolated from a humic lake.  

PubMed

A Gram-negative, rod-shaped, non-spore-forming betaproteobacterium (TRO-001DR8T) was isolated from humic-lake samples collected from northern Wisconsin, USA. On the basis of 16S rRNA gene sequence analysis, strain TRO-001DR8T belonged to the family Neisseriaceae, and the phylogenetic distance from its closest relative, Chromobacterium violaceum, was 95 %. Strain TRO-001DR8T lacked the violet pigmentation of C. violaceum and shared only 26 % DNA-DNA relatedness with C. violaceum. The DNA G+C content of strain TRO-001DR8T was 59 mol%. The predominant fatty acids were C(16 : 1)omega7c + C(16 : 1)omega7c 2-OH iso (52.5 %), C(16 : 0) (21.7 %), C(18 : 1)omega7c (8.0 %) and C(12 : 0) (5.1 %). Strain TRO-001DR8T grew optimally at 35 degrees C and pH 6.0, did not utilize sucrose, but did use glucose, some organic acids and most protein amino acids. Biochemical, physiological, chemotaxonomic and phylogenetic analyses showed that strain TRO-001DR8T could not be assigned to any known genus of the Betaproteobacteria. Therefore, the isolate represents a novel genus and species, for which the name Aquitalea magnusonii gen. nov., sp. nov. is proposed. The type strain is TRO-001DR8T (=ATCC BAA-1216T = BCCM/LMG 23054T). PMID:16585708

Lau, Hoi-Ting; Faryna, John; Triplett, Eric W

2006-04-01

356

Deferribacter thermophilus gen. nov., sp. nov., a novel thermophilic manganese- and iron-reducing bacterium isolated from a petroleum reservoir.  

PubMed

A thermophilic anaerobic bacterium, designated strain BMAT (T = type strain), was isolated from the production water of Beatrice oil field in the North Sea (United Kingdom). The cells were straight to bent rods (1 to 5 by 0.3 to 0.5 microns) which stained gram negative. Strain BMAT obtained energy from the reduction of manganese (IV), iron(III), and nitrate in the presence of yeast extract, peptone, Casamino Acids, tryptone, hydrogen, malate, acetate, citrate, pyruvate, lactate, succinate, and valerate. The isolate grew optimally at 60 degrees C (temperature range for growth, 50 to 65 degrees C) and in the presence of 2% (wt/vol) NaCl (NaCl range for growth, 0 to 5% [wt/vol]). The DNA base composition was 34 mol% G + C. Phylogenetic analyses of the 16S rRNA gene indicated that strain BMAT is a member of the domain Bacteria. The closest known bacterium is the moderate thermophile Flexistipes sinusarabici (similarity value, 88%). Strain BMAT possesses phenotypic and phylogenetic traits that do not allow its classification as a member of any previously described genus; therefore, we propose that this isolate should be described as a member of a novel species of a new genus, Deferribacter thermophilus gen. nov., sp. nov. PMID:9103640

Greene, A C; Patel, B K; Sheehy, A J

1997-04-01

357

Moorea producens gen. nov., sp. nov. and Moorea bouillonii comb. nov., tropical marine cyanobacteria rich in bioactive secondary metabolites.  

PubMed

The filamentous cyanobacterial genus Moorea gen. nov., described here under the provisions of the International Code of Botanical Nomenclature, is a cosmopolitan pan-tropical group abundant in the marine benthos. Members of the genus Moorea are photosynthetic (containing phycocyanin, phycoerythrin, allophycocyanin and chlorophyll a), but non-diazotrophic (lack heterocysts and nitrogenase reductase genes). The cells (discoid and 25-80 µm wide) are arranged in long filaments (<10 cm in length) and often form extensive mats or blooms in shallow water. The cells are surrounded by thick polysaccharide sheaths covered by a rich diversity of heterotrophic micro-organisms. A distinctive character of this genus is its extraordinarily rich production of bioactive secondary metabolites. This is matched by genomes rich in polyketide synthase and non-ribosomal peptide synthetase biosynthetic genes which are dedicated to secondary metabolism. The encoded natural products are sometimes responsible for harmful algae blooms and, due to morphological resemblance to the genus Lyngbya, this group has often been incorrectly cited in the literature. We here describe two species of the genus Moorea: Moorea producens sp. nov. (type species of the genus) with 3L(T) as the nomenclature type, and Moorea bouillonii comb. nov. with PNG5-198(R) as the nomenclature type. PMID:21724952

Engene, Niclas; Rottacker, Erin C; Kaštovský, Jan; Byrum, Tara; Choi, Hyukjae; Ellisman, Mark H; Komárek, Ji?í; Gerwick, William H

2011-07-01

358

Copy number variations associated with obesity related traits in African Americans: a joint analysis between GENOA and HyperGEN  

PubMed Central

Obesity is a highly heritable trait and a growing public health problem. African Americans are a genetically diverse, yet understudied population with a high prevalence of obesity (body mass index (BMI) greater than 30 kg/m2). Recent studies based upon single nucleotide polymorphisms (SNPs) have identified genetic markers associated with obesity. However, a large proportion of the heritability of obesity remains unexplained. Copy number variation (CNV) has been cited as a possible source of missing heritability in common diseases such as obesity. We conducted a CNV genome-wide association study of BMI in two African American cohorts from GENOA and HyperGEN. We performed independent and identical association analyses in each study, then combined the results in a meta-analysis. We identified three CNVs associated with BMI, obesity, and other obesity-related traits after adjusting for multiple testing. These CNVs overlap the PARK2, GYPA and SGCZ genes. Our results suggest that CNV may play a role in the etiology of obesity in African Americans.

Zhao, Wei; Wineinger, Nathan E.; Tiwari, Hemant K.; Mosley, Thomas H.; Broeckel, Ulrich; Arnett, Donna K.; Kardia, Sharon L. R.; Kabagambe, Edmond K.; Sun, Yan V.

2012-01-01

359

bc-GenExMiner 3.0: new mining module computes breast cancer gene expression correlation analyses  

PubMed Central

We recently developed a user-friendly web-based application called bc-GenExMiner (http://bcgenex.centregauducheau.fr), which offered the possibility to evaluate prognostic informativity of genes in breast cancer by means of a ‘prognostic module’. In this study, we develop a new module called ‘correlation module’, which includes three kinds of gene expression correlation analyses. The first one computes correlation coefficient between 2 or more (up to 10) chosen genes. The second one produces two lists of genes that are most correlated (positively and negatively) to a ‘tested’ gene. A gene ontology (GO) mining function is also proposed to explore GO ‘biological process’, ‘molecular function’ and ‘cellular component’ terms enrichment for the output lists of most correlated genes. The third one explores gene expression correlation between the 15 telomeric and 15 centromeric genes surrounding a ‘tested’ gene. These correlation analyses can be performed in different groups of patients: all patients (without any subtyping), in molecular subtypes (basal-like, HER2+, luminal A and luminal B) and according to oestrogen receptor status. Validation tests based on published data showed that these automatized analyses lead to results consistent with studies’ conclusions. In brief, this new module has been developed to help basic researchers explore molecular mechanisms of breast cancer. Database URL: http://bcgenex.centregauducheau.fr

Jezequel, Pascal; Frenel, Jean-Sebastien; Campion, Loic; Guerin-Charbonnel, Catherine; Gouraud, Wilfried; Ricolleau, Gabriel; Campone, Mario

2013-01-01

360

Methylibium petroleiphilum gen. nov., sp. nov., a novel methyl tert-butyl ether-degrading methylotroph of the Betaproteobacteria.  

PubMed

A Gram-negative, rod-shaped, motile, non-pigmented, facultative aerobe that grew optimally at pH 6.5 and 30 degrees C (strain PM1T) was isolated for its ability to completely degrade the gasoline additive methyl tert-butyl ether. Analysis of the 16S rRNA gene sequence indicated that this bacterium was a member of the class Betaproteobacteria in the Sphaerotilus-Leptothrix group. The 16S rRNA gene sequence identity to other genera in this group, Leptothrix, Aquabacterium, Roseateles, Sphaerotilus, Ideonella and Rubrivivax, ranged from 93 to 96 %. The chemotaxonomic data including Q-8 as the major quinone, C16 : 1omega7c and C16 : 0 as the major fatty acids and a DNA G+C content of 69 mol%, support the inclusion of strain PM1T in the class Betaproteobacteria. It differed from other members of the Sphaerotilus-Leptothrix group by being a facultative methylotroph that used methanol as a sole carbon source, and by also being able to grow heterotrophically in defined media containing ethanol, toluene, benzene, ethylbenzene and dihydroxybenzoates as sole carbon sources. On the basis of the morphological, physiological, biochemical and genetic information, a new genus and species, Methylibium petroleiphilum gen. nov., sp. nov., is proposed, with PM1T (=ATCC BAA-1232T=LMG 22953T) as the type strain. PMID:16627642

Nakatsu, Cindy H; Hristova, Krassimira; Hanada, Satoshi; Meng, Xian-Ying; Hanson, Jessica R; Scow, Kate M; Kamagata, Yoichi

2006-05-01

361

Ignisphaera aggregans gen. nov., sp. nov., a novel hyperthermophilic crenarchaeote isolated from hot springs in Rotorua and Tokaanu, New Zealand.  

PubMed

Consortia containing a novel coccus-shaped, anaerobic heterotroph together with Pyrobaculum rods were cultivated from geothermal environments in New Zealand. Pure cultures of the cocci were only obtained from one such consortium, despite extensive attempts. Cells of this strain (AQ1.S1T) were regular to irregular cocci in morphology and occasionally formed large aggregates, especially when utilizing polysaccharides such as konjac glucomannan as a carbon source. Strain AQ1.S1T is a hyperthermophile, with an optimal temperature for growth between 92 and 95 degrees C (range 85-98 degrees C), and a moderate acidophile, with optimal growth occurring at pH 6.4 (range 5.4-7.0). Growth was inhibited by the addition of sulphur and NaCl (optimal growth occurred without addition of NaCl) and an electron acceptor was not required. Strain AQ1.S1T utilized starch, trypticase peptone, lactose, glucose, konjac glucomannan, mannose, galactose, maltose, glycogen and beta-cyclodextrin as carbon sources. The G+C content was 52.9 mol%. Based on 16S rRNA gene sequence analysis and physiological features it is proposed that isolate AQ1.S1T (=DSM 17230T=JCM 13409T) represents the type strain of a novel species of a new genus within the Crenarchaeota, Ignisphaera aggregans gen. nov., sp. nov. PMID:16627639

Niederberger, Thomas D; Götz, Dorothee K; McDonald, Ian R; Ronimus, Ron S; Morgan, Hugh W

2006-05-01

362

Palpitomonas bilix gen. et sp. nov.: A novel deep-branching heterotroph possibly related to Archaeplastida or Hacrobia.  

PubMed

We describe the ultrastructure and putative molecular phylogenetic position of a free-living heterotrophic flagellate Palpitomonas bilix gen. et sp. nov. This flagellate is 3-8mum in size, and possesses two subequal flagella, approximately 20mum long. Electron microscopical observations revealed that the flagellar apparatus of P. bilix resembles that of members of the green algal class, Charophyceae, while the mastigonemes of the P. bilix flagellum share some characteristics with those found in cryptophytes and telonemids. In order to better understand the phylogenetic position of P. bilix, we sequenced six commonly used phylogenetic marker genes encoding the small and large subunits of ribosomal RNA, alpha-tubulin, beta-tubulin, 90kDa heat shock protein, and translation elongation factor 2. Depending on the genes analyzed, P. bilix shows a generally weak phylogenetic affinity to either the newly erected Hacrobia, which includes cryptophytes and haptophytes, or to Archaeplastida. Since the current study identified no clear close relative of P. bilix, this novel biflagellate was classified into a new genus Palpitomonas with the higher-level classification being unclear. On the basis of the results of both morphological and molecular studies, we discuss the possibility that P. bilix might provide key information on the early evolution of major groups of photosynthetic eukaryotes. PMID:20418156

Yabuki, Akinori; Inagaki, Yuji; Ishida, Ken-ichiro

2010-04-24

363

Revision of the Genus Coriplites Foissner, 1988 (Ciliophora: Haptorida), with Description of Apocoriplites nov. gen. and Three New Species  

PubMed Central

Summary The genera Coriplites Foissner, 1988 and Apocoriplites nov. gen., which differ by the number of dorsal brush rows (3 vs. 2), belong to the haptorid Litostomatea and have a distinct feature in common: they lack oral extrusomes. Based on three new species, the diagnosis of the genus Coriplites is amended to include the wide spacing of the brush dikinetids and the heavily refractive cortical granules. Using standard methods, we redescribe C. terricola Foissner, 1988 and describe three new species: C. grandis (from swamp soil of Australia), C. proctori (from tanks of bromeliads in Jamaica), and Apocoriplites lajacola (from granitic rook-pools in Venezuela). Species are distinguished by the nuclear apparatus (a single nodule vs. two nodules with a micronucleus in between), the body size (<100 ?m vs. >100 ?m), the number of ciliary rows, and details of the dorsal brush (isostichad vs. heterostichad). In over 1,000 soil samples, only C. terricola has been found in all main biogeographic regions, while the other species have been found only at their type locality, i.e., in the southern hemisphere, where the genus possibly originated.

OERTEL, Anke; WOLF, Klaus; AL-RASHEID, Khaled; FOISSNER, Wilhelm

2010-01-01

364

Enhygromyxa salina gen. nov., sp. nov., a slightly halophilic myxobacterium isolated from the coastal areas of Japan.  

PubMed

Six isolates of novel marine myxobacteria, designated strains SHK-1T, SMK-1-1, SMK-1-3, SMK-10, SKK-2, and SMP-6, were obtained from various coastal samples (mud, sands and algae) collected around Japan. All of the isolates had Gram-negative rod-shaped cells, motile by gliding and grew aerobically. They showed bacteriolytic action, fruiting body formation, and NaCl requirement for growth with an optimum concentration of 1.0-2.0% (w/v). In addition, divalent cationic components of seawater, such as Mg2+ or Ca2+, were also needed for growth. The major respiratory quinone was MK-7. The G+C content of genomic DNA ranged from 65.6 to 67.4 mol% (by HPLC). The isolates shared almost identical 16S rDNA sequences, and clustered with a recently described marine myxobacterium, Plesiocystis pacifica, as their closest relative on a phylogenetic tree (95.9-96.0% similarity). Physiological and chemotaxonomic differences between the new strains and strains of the genus Plesiocystis justify the proposal of a new genus. Therefore, we propose to classify the six isolates into a new taxon of marine myxobacteria with the name, Enhygromyxa salina gen. nov., sp. nov. The type strain is SHK-1(T) (JCM 11769(T) = DSM 15217(T) = AJ 110011(T)). PMID:12866845

Iizuka, Takashi; Jojima, Yasuko; Fudou, Ryosuke; Tokura, Mitsunori; Hiraishi, Akira; Yamanaka, Shigeru

2003-06-01

365

Nicoletella semolina gen. nov., sp. nov., a New Member of Pasteurellaceae Isolated from Horses with Airway Disease  

PubMed Central

Gram-negative, nonmotile bacteria that are catalase, oxidase, and urease positive are regularly isolated from the airways of horses with clinical signs of respiratory disease. On the basis of the findings by a polyphasic approach, we propose that these strains be classified as Nicoletella semolina gen. nov, sp. nov., a new member of the family Pasteurellaceae. N. semolina reduces nitrate to nitrite but is otherwise biochemically inert; this includes the lack of an ability to ferment glucose and other sugars. Growth is fastidious, and the isolates have a distinctive colony morphology, with the colonies being dry and waxy and looking like a semolina particle that can be moved around on an agar plate without losing their shape. DNA-DNA hybridization data and multilocus phylogenetic analysis, including 16S rRNA gene (rDNA), rpoB, and infB sequencing, clearly placed N. semolina as a new genus in the family Pasteurellaceae. In all the phylogenetic trees constructed, N. semolina is on a distinct branch displaying ?5% 16S rDNA, ?16% rpoB, and ?20% infB sequence divergence from its nearest relative within the family Pasteurellaceae. High degrees of conservation of the 16S rDNA (99.8%), rpoB (99.6%), and infB (99.7%) sequences exist within the species, indicating that N. semolina isolates not only are phenotypically homogeneous but also are genetically homogeneous. The type strain of N. semolina is CCUG43639T (DSM16380T).

Kuhnert, Peter; Korczak, Bozena; Falsen, Enevold; Straub, Reto; Hoops, Anneliese; Boerlin, Patrick; Frey, Joachim; Mutters, Reinier

2004-01-01

366

Alkaliphilus transvaalensis gen. nov., sp. nov., an extremely alkaliphilic bacterium isolated from a deep South African gold mine  

SciTech Connect

A novel extreme alkaliphile was isolated from a mine water containment dam at 3.2 km bellow land surface in an ultra-deep gold mine near Carletonville, South Africa. The cells of this bacterium were straight to slightly curved rods, motile by flagella and formed endospores, Growth was observed over the temperature range 20-50 degreesC (optimum 40 degreesC; 45 min doubling time) and ph range 8.5-12.5 (optimum pH 10.0). The novel isolate, one of the most alkaliphilic micro-organisms yet described, was a strictly anaerobic chemo-organotroph capable of utilizing proteinaceous substrates such as yeast extract, peptone. tryptone and casein, Elemental sulfur, thiosulfate or fumarate, when included as accessory electron acceptors, improved growth. The G+C content of genomic DNA was 36.4 mol%, Phylogenetic analysis based on the 16S rDNA sequence indicated that the isolate is a member of cluster XI within the low G+C Cram-positive bacteria, but only distantly related to previously described members. On the basis of physiological and molecular properties, the isolate represents a novel species, for which the name Alkaliphilus transvaalensis gen. nov., sp. nov. is proposed (type strain SAGM1(T)= JCM 10712(T)= ATCC 700919(T)). The mechanism of generation of the highly alkaline microbial habitat and the possible source of the alkaliphile are discussed.

Takai, Ken; Moser, Duane P.; Onstott, Tullis C.; Spoelstra, N; Pfiffner, Susan M.; Dohnalkova, Alice; Fredrickson, Jim K.

2001-07-01

367

Humitalea rosea gen. nov., sp. nov., an aerobic bacteriochlorophyll-containing bacterium of the family Acetobacteraceae isolated from soil.  

PubMed

A Gram-staining-negative, pale-pink-pigmented, non-motile, obligately aerobic and rod-shaped bacterium, designated strain W37(T), was isolated from soil and subjected to a taxonomic investigation using a polyphasic approach. The strain grew at 1-30 °C, oxidized thiosulfate and accumulated polyhydroxyalkanoates. Photosynthetic pigments were represented by bacteriochlorophyll a and carotenoids. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain W37(T) was most closely related to members of the genera Roseococcus and Rubritepida (with sequence similarities of <92.8?%) but formed a distinct lineage in the family Acetobacteraceae. The polar lipid profile comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, three unidentified aminolipids and one other unidentified lipid. The predominant cellular fatty acids were C18?:?1?7c and summed feature 3 (C16?:?1?7c and/or iso-C15?:?0 2-OH). The DNA G+C content of strain W37(T) was 68.2 mol%. On the basis of phenotypic characteristics and phylogenetic analysis, strain W37(T) represents a novel species of a new genus in the family Acetobacteraceae, for which the name Humitalea rosea gen. nov., sp. nov. is proposed. The type strain of the type species is W37(T) (?=?CIP 110261(T)?=?LMG 26243(T)). PMID:22821736

Margesin, Rosa; Zhang, De-Chao

2012-07-20

368

Rehaibacterium terrae gen. nov., sp. nov. isolated from a geothermally heated soil sample in Tengchong, Yunnan, south-west China.  

PubMed

A thermotolerant, alkalitolerant, Gram-negative and strictly aerobic bacterium, designated strain YIM 77974T, was isolated from a geothermally heated soil sample collected at Rehai National Park, Tengchong, Yunnan province, south-west China. Cells of the strain were rod-shaped and colonies were light brown and circular. The strain grew in the presence of 0-3% (w/v) NaCl (optimum, 0-1%) and at pH 7.0-10.0 (optimum, pH 8.0) and 30-55 °C (optimum, 45 °C). The only quinone was Q-8 and the genomic DNA G+C content was 68.3 mol%. Major fatty acids (>10 %) were iso-C16:0, iso-C17:0, iso-C15:0 and iso-C11:0. The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, unidentified aminophospholipid, three unidentified phospholipids and two unidentified polar lipids. On the basis of the morphological and chemotaxonomic characteristics as well as genotypic data, it is proposed that this strain should be classified as a novel genus and species, Rehaibacterium terrae gen. nov., sp. nov., in the family Xanthomonadaceae. The type strain is strain YIM 77974T (=DSM 25897T=CCTCC AB 2012062T). PMID:23771618

Yu, Tian-Tian; Yao, Ji-Cheng; Yin, Yi-Rui; Dong, Lei; Liu, Ruo-Fei; Ming, Hong; Zhou, En-Min; Li, Wen-Jun

2013-06-14

369

Oleispira antarctica gen. nov., sp. nov., a novel hydrocarbonoclastic marine bacterium isolated from Antarctic coastal sea water.  

PubMed

The taxonomic characteristics of two bacterial strains, RB-8(T) and RB-9, isolated from hydrocarbon-degrading enrichment cultures obtained from Antarctic coastal marine environments (Rod Bay, Ross Sea), were determined. These bacteria were psychrophilic, aerobic and Gram-negative with polar flagella. Growth was not observed in the absence of NaCl, occurred only at concentrations of Na+ above 20 mM and was optimal at an NaCl concentration of 3-5% (w/v). The major cellular fatty acids were monounsaturated straight-chain fatty acids. The strains were able to synthesize the polyunsaturated fatty acid eicosapentaenoic acid (20: 5omega3) at low temperatures. The DNA G + C contents were 41-42 mol%. The strains formed a distinct phyletic line within the gamma-Proteobacteria, with less than 89.6% sequence identity to their closest relatives within the Bacteria with validly published names. Both isolates exhibited a restricted substrate profile, with a preference for aliphatic hydrocarbons, that is typical of marine hydrocarbonoclastic micro-organisms such as Alcanivorax, Marinobacter and Oleiphilus. On the basis of ecophysiological properties, G + C content, 16S rRNA gene sequences and fatty acid composition, a novel genus and species within the gamma-Proteobacteria are proposed, Oleispira antarctica gen. nov., sp. nov.; strain RB-8(T) (= DSM 14852(T) = LMG 21398(T)) is the type strain. PMID:12807200

Yakimov, Michail M; Giuliano, Laura; Gentile, Gabriella; Crisafi, Ermanno; Chernikova, Tatyana N; Abraham, Wolf-Rainer; Lünsdorf, Heinrich; Timmis, Kenneth N; Golyshin, Peter N

2003-05-01

370

Characterization of the anaerobic propionate-degrading syntrophs Smithella propionica gen. nov., sp. nov. and Syntrophobacter wolinii.  

PubMed

A strain of anaerobic, syntrophic, propionate-oxidizing bacteria, strain LYPT (= OCM 661T; T = type strain), was isolated and proposed as representative of a new genus and new species, Smithella propionica gen. nov., sp. nov. The strain was enriched from an anaerobic digestor and isolated. Initial isolation was as a monoxenic propionate-degrading co-culture containing Methanospirillum hungateii JF-1T as an H2- and formate-using partner. Later, an axenic culture was obtained by using crotonate as the catabolic substrate. The previously described propionate-degrading syntrophs of the genus Syntrophobacter also grow in co-culture with methanogens such as Methanospirillum hungateii, forming acetate, CO2 and methane from propionate. However, Smithella propionica differs by producing less methane and more acetate; in addition, it forms small amounts of butyrate. Smithella propionica and Syntrophobacter wolinii grew within similar ranges of pH, temperature and salinity, but they differed significantly in substrate ranges and catabolic products. Unlike Syntrophobacter wolinii, Smithella propionica grew axenically on crotonate, although very slowly. Co-cultures of Smithella propionica grew on propionate, and grew slowly on crotonate or butyrate. Syntrophobacter wolinii and Syntrophobacter pfennigii grow on propionate plus sulfate, whereas Smithella propionica did not. Comparisons of 16S rDNA genes indicated that Smithella propionica is most closely related to Syntrophus, and is more distantly related to Syntrophobacter. PMID:10319475

Liu, Y; Balkwill, D L; Aldrich, H C; Drake, G R; Boone, D R

1999-04-01

371

Evaluation of Copan Swabs with Liquid Transport Media for Use in the Gen-Probe Group A Strep Direct Test  

PubMed Central

The Gen-Probe Group A Streptococcus Direct Test (GASDT), which detects the presence or absence of group A streptococci directly from pharyngeal specimens, utilizes a specific relative light unit (RLU) cutoff of 4,500 to differentiate between positive and negative test results. In response to a report by a manufacturer that the background RLU values for the Copan rayon swabs with liquid media were higher than the RLU values typically observed with Culturette swabs, we tested multiple lots of Copan rayon swabs with liquid media and determined that the swabs are unacceptable for routine use in the GASDT. The high background RLU values for the Copan rayon swabs appear to be a direct result of the gamma irradiation used to sterilize the swabs. We also performed a comparative clinical evaluation of Copan Dacron swabs with liquid media and Culturette swabs for use in the GASDT. Overall, there was 97.5% agreement between the results obtained with the Copan Dacron swabs and those obtained with the Culturette swabs. Compared to Culturette swabs, the Copan Dacron swabs had a sensitivity and a specificity of 97 and 98%, respectively. Copan Dacron swabs with liquid media are an acceptable alternative to the swabs currently qualified for use with the GASDT, but Copan rayon swabs with liquid transport media should not be used in the GASDT.

Bourbeau, Paul P.; Heiter, Barbara J.

2003-01-01

372

Rubidimonas crustatorum gen. nov., sp. nov., a novel member of the family Saprospiraceae isolated from a marine crustacean.  

PubMed

A strictly aerobic, Gram-negative, reddish-orange pigmented, non-motile and rod-shaped bacterium, designated AK17-053(T) was isolated from a marine crustacean (Squillidae) living on tidal flats on the coast of the Ariake Sea, Nagasaki, Japan. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that the novel isolate could be affiliated with the family Saprospiraceae of the phylum Bacteroidetes and that it showed highest sequence similarity (84%) with Lewinella marina MKG-38(T). The strain could be differentiated phenotypically from recognized members of the family Saprospiraceae. The G+C content of DNA was 55.3 mol%, MK-7 was the major menaquinone and iso-C(15:0) and C(16:1)?7c were the major fatty acids. On the basis of polyphasic taxonomic studies, it was concluded that strain AK17-053(T) represents a new genus of the family Saprospiraceae. We propose the name Rubidimonas crustatorum gen. nov., sp. nov. for this strain; its type strain is AK17-053(T) (= MBIC08356(T) = NBRC 107717(T)). PMID:21993690

Yoon, Jaewoo; Katsuta, Atsuko; Kasai, Hiroaki

2011-10-13

373

Moorea producens gen. nov., sp. nov. and Moorea bouillonii comb. nov., tropical marine cyanobacteria rich in bioactive secondary metabolites  

PubMed Central

The filamentous cyanobacterial genus Moorea gen. nov., described here under the provisions of the International Code of Botanical Nomenclature, is a cosmopolitan pan-tropical group abundant in the marine benthos. Members of the genus Moorea are photosynthetic (containing phycocyanin, phycoerythrin, allophycocyanin and chlorophyll a), but non-diazotrophic (lack heterocysts and nitrogenase reductase genes). The cells (discoid and 25–80 µm wide) are arranged in long filaments (<10 cm in length) and often form extensive mats or blooms in shallow water. The cells are surrounded by thick polysaccharide sheaths covered by a rich diversity of heterotrophic micro-organisms. A distinctive character of this genus is its extraordinarily rich production of bioactive secondary metabolites. This is matched by genomes rich in polyketide synthase and non-ribosomal peptide synthetase biosynthetic genes which are dedicated to secondary metabolism. The encoded natural products are sometimes responsible for harmful algae blooms and, due to morphological resemblance to the genus Lyngbya, this group has often been incorrectly cited in the literature. We here describe two species of the genus Moorea: Moorea producens sp. nov. (type species of the genus) with 3LT as the nomenclature type, and Moorea bouillonii comb. nov. with PNG5-198R as the nomenclature type.

Engene, Niclas; Rottacker, Erin C.; Kastovsky, Jan; Byrum, Tara; Choi, Hyukjae; Ellisman, Mark H.; Komarek, Jiri

2012-01-01

374

Genome-wide joint SNP and CNV analysis of aortic root diameter in African Americans: the HyperGEN study  

PubMed Central

Background Aortic root diameter is a clinically relevant trait due to its known relationship with the pathogenesis of aortic regurgitation and risk for aortic dissection. African Americans are an understudied population despite a particularly high burden of cardiovascular diseases. We report a genome-wide association study on aortic root diameter among African Americans enrolled in the HyperGEN study. We invoked a two-stage, mixed model procedure to jointly identify SNP allele and copy number variation effects. Results Results suggest novel genetic contributors along a large region between the CRCP and KCTD7 genes on chromosome 7 (p = 4.26 × 10-7); and the SIRPA and PDYN genes on chromosome 20 (p = 3.28 × 10-8). Conclusions The regions we discovered are candidates for future studies on cardiovascular outcomes, particularly in African Americans. The methods we employed can also provide an outline for genetic researchers interested in jointly testing SNP and CNV effects and/or applying mixed model procedures on a genome-wide scale.

2011-01-01

375

Chelonacarus elongatus n. gen., n. sp. (Acari: Cloacaridae) from the cloaca of the green turtle Chelonia mydas (Cheloniidae).  

PubMed

Chelonacarus elongatus n. gen., n. sp. is proposed for a cheyletoid mite (Acari: Prostigmata) of the family Cloacaridae found in the cloacal tissue of the endangered green turtle Chelonia mydas Linnaeus, 1758 from the Atlantic coast of the Republic of Panama. In females, the new genus is distinguished from other genera of turtle cloacarids by the elongate slender shape of the idiosoma, the shape and pattern of sclerotization of the dorsal shield, and the fused distal ends of apodemes II. A combination of other features that distinguish the newly proposed genus is the smooth surface of the pedipalps, single dorsal spine on tibiae I-IV, no setae on coxa IV, terminal position of the vulva, and the strongly developed pair of ventral spines on tarsi I-II. This is the first record of cloacarids from sea turtles. The similarity of adult cloacarids in the genus Chelonacarus from sea turtles (Chelonioidea) and Cloacarus Camin et al., 1967 from snapping turtles (Chelydridae) lends support to the hypothesis of some paleontologists that these 2 groups of turtles are linked phylogenetically. PMID:9714221

Pence, D B; Wright, S D

1998-08-01

376

Ultrastructure and LSU rDNA-based phylogeny of Peridinium lomnickii and description of Chimonodinium gen. nov. (Dinophyceae).  

PubMed

Several populations of Peridinium lomnickii were examined by SEM and serial section TEM. Comparison with typical Peridinium, Peridiniopsis, Palatinus and Scrippsiella species revealed significant structural differences, congruent with phylogenetic hypotheses derived from partial LSU rDNA sequences. Chimonodinium gen. nov. is described as a new genus of peridinioids, characterized by the Kofoidian plate formula Po, cp, x, 4', 3a, 7'', 6c, 5s, 5''', 2'''', the absence of pyrenoids, the presence of a microtubular basket with four or five overlapping rows of microtubules associated with a small peduncle, a pusular system with well-defined pusular tubes connected to the flagellar canals, and the production of non-calcareous cysts. Serial section examination of Scrippsiella trochoidea, here taken to represent typical Scrippsiella characters, revealed no peduncle and no associated microtubular strands. The molecular phylogeny placed C. lomnickii comb. nov. as a sister group to a clade composed of Thoracosphaera and the pfiesteriaceans. Whereas the lack of information on fine structure of the swimming stage of Thoracosphaera leaves its affinities unexplained, C. lomnickii shares with the pfiesteriaceans the presence of a microtubular basket and the unusual connection between two plates on the left side of the sulcus, involving extra-cytoplasmic fibres. PMID:21621455

Craveiro, Sandra C; Calado, António J; Daugbjerg, Niels; Hansen, Gert; Moestrup, Øjvind

2011-05-28

377

Tanticharoenia sakaeratensis gen. nov., sp. nov., a new osmotolerant acetic acid bacterium in the alpha-Proteobacteria.  

PubMed

Tanticharoenia sakaeratensis gen. nov., sp. nov. is proposed for three strains isolated from soil collected in Thailand. The three strains, AC37(T), AC38, and AC39, were included within a lineage comprising the genera Asaia, Kozakia, Swaminathania, Neoasaia, Acetobacter, Gluconobacter, and Saccharibacter in a phylogenetic tree based on 16S rRNA gene sequences, but formed a quite different, independent cluster. Pair-wise sequence similarities of strain AC37(T) were 96.5-92.1% to the type strains of Acetobacter aceti, Gluconobacter oxydans, Acidomonas methanolica, Gluconacetobacter liquefaciens, Asaia bogorensis, Kozakia baliensis, Swaminathania salitolerans, Saccharibacter floricola, Neoasaia chiangmaiensis, and Granulibacter bethesdensis. The three strains had DNA base compositions comprising respectively 65.6, 64.5, and 65.6 mol % G+C with a range of 1.1 mol %, and formed a single species. Phenotypically, the three strains did not oxidize acetate or lactate, but grew on 30% D-glucose (w/v). Chemotaxonomically, they had Q-10. The type strain is AC37(T) (= BCC 15772(T) = NBRC 103193(T)). PMID:18323667

Yukphan, Pattaraporn; Malimas, Taweesak; Muramatsu, Yuki; Takahashi, Mai; Kaneyasu, Mika; Tanasupawat, Somboon; Nakagawa, Yasuyoshi; Suzuki, Ken-ichiro; Potacharoen, Wanchern; Yamada, Yuzo

2008-03-07

378

Cipactlichthys scutatus, gen. nov., sp. nov. a new Halecomorph (Neopterygii, Holostei) from the Lower Cretaceous Tlayua Formation of Mexico.  

PubMed

Based on specimens from the Lower Cretaceous Tlayua Formation of Mexico, we describe a new genus and species of Halecomorphi, Cipactlichthysscutatus gen. et sp. nov, which exhibits several diagnostic characters such as the dermal bones and the scales with ganoin and highly ornamented by numerous tubercles and ridges; parietal slightly longer than wide with approximately the same length as the frontal; jaws extending far, below the posterior orbital margin, reaching the posterior third of the postorbital plate; maxilla with a convexly rounded posterior margin; pectoral fin margins slightly convex; first ray of pectoral fin very long, reaching the posterior edge of the pelvic fin; about 37 preural vertebrae and 7 Ural centra; a series of hypertrophied scales just posterior to the cleithrum; arrangement of flank scales with two rows of deep scales; a series of dorsal and ventral scutes forming the dorsal and ventral midline, between the dorsal and anal fins and the caudal fin. A phylogenetic analysis including two outgroups and eleven neopterygians confirmed the monophyly of the Holostei as well as the monophyly of the Halecomorphi, although this last clade is weakly supported. Cipactlichthysscutatus was hypothesised as the sister-group of the (Ionoscopiformes + Amiiformes). PMID:24023885

Brito, Paulo M; Alvarado-Ortega, Jesus

2013-09-04

379

Arenitalea lutea gen. nov., sp. nov., a marine bacterium of the family Flavobacteriaceae isolated from intertidal sand.  

PubMed

A yellow, rod-shaped, Gram-negative, facultatively aerobic, gliding bacterium, designed strain P7-3-5(T), was isolated from intertidal sand of the Yellow Sea, China. Analysis of 16S rRNA gene sequences revealed that strain P7-3-5(T) formed a distinct lineage within the family Flavobacteriaceae, sharing 94.2-96.9 % sequence similarity with type strains of species of the most closely related genera, including Hyunsoonleella, Jejuia, Marinivirga and Algibacter. The strain grew at 4-40 °C and with 0.5-5.0 % (w/v) NaCl. It reduced nitrate to nitrite and hydrolysed gelatin and DNA. The major cellular fatty acids were iso-C15 : 0, iso-C15 : 1 G and anteiso-C15 : 0 and the major respiratory quinone was MK-6. Polar lipids included phosphatidylethanolamine (PE), three unidentified aminolipids (AL1-3) and four unidentified lipids (L1-4). The genomic DNA G+C content of strain P7-3-5(T) was 32.1 mol%. Data from this polyphasic study suggest that strain P7-3-5(T) represents a novel species in a new genus in the family Flavobacteriaceae, for which the name Arenitalea lutea gen. nov., sp. nov. is proposed. The type strain of Arenitalea lutea is P7-3-5(T) ( = CGMCC 1.12213(T) = KACC 16457(T)). PMID:23315415

Zhang, Xi-Ying; Liu, Ang; Liu, Chang; Li, Hai; Li, Guo-Wei; Xu, Zhong; Chen, Xiu-Lan; Zhou, Bai-Cheng; Zhang, Yu-Zhong

2013-01-11

380

Vetufebrus ovatus n. gen., n. sp. (Haemospororida: Plasmodiidae) vectored by a streblid bat fly (Diptera: Streblidae) in Dominican amber  

PubMed Central

Background Both sexes of bat flies in the families Nycteribiidae and Streblidae (Diptera: Hippoboscoidea) reside in the hair or on the wing membranes of bats and feed on blood. Members of the Nycteribiidae transmit bat malaria globally however extant streblids have never been implemented as vectors of bat malaria. The present study shows that during the Tertiary, streblids also were vectors of bat malaria. Results A new haemospororidan, Vetufebrus ovatus, n. gen., n. sp., (Haemospororida: Plasmodiidae) is described from two oocysts attached to the midgut wall and sporozoites in salivary glands and ducts of a fossil bat fly (Diptera: Streblidae) in Dominican amber. The new genus is characterized by ovoid oocysts, short, stubby sporozoites with rounded ends and its occurrence in a fossil streblid. This is the first haemosporidian reported from a streblid bat fly and shows that representatives of the Hippoboscoidea were vectoring bat malaria in the New World by the mid-Tertiary. Conclusions This report is the first evidence of an extant or extinct streblid bat fly transmitting malaria. Discovering a mid-tertiary malarial parasite in a fossil streblid that closely resembles members of a malarial genus found in nycteribiid bat flies today shows how little we know about the vector associations of streblids. While no malaria parasites have been found in extant streblids, they probably occur and it is possible that streblids were the earliest lineage of flies that transmitted bat malaria to Chiroptera.

2011-01-01

381

Haloalkaliphilic spore-forming sulfidogens from soda lake sediments and description of Desulfitispora alkaliphila gen. nov., sp. nov.  

PubMed Central

An anaerobic enrichment with pyruvate as electron donor and thiosulfate at pH 10 and 0.6 M Na+ inoculated with pasteurized soda lake sediments resulted in a sulfidogenic coculture of two morphotypes of obligately anaerobic haloalkaliphilic endospore-forming clostridia, which were further isolated in pure culture. Strain AHT16 was a thin long rod able to ferment sugars and pyruvate and to respire H2, formate and pyruvate using thiosulfate and fumarate as electron acceptors and growing optimally at pH 9.5. Thiosulfate was reduced incompletely to sulfide and sulfite. The strain was closely related (99% sequence similarity) to a peptolytic alkaliphilic clostridium Natronincola peptidovorans. Strain AHT17 was a short rod with a restricted respiratory metabolism, growing with pyruvate and lactate as electron donor and sulfite, thiosulfate and elemental sulfur as electron acceptors with a pH optimum 9.5. Thiosulfate was reduced completely via sulfite to sulfide. The ability of AHT17 to use sulfite explained the stability of the original coculture of the two clostridia—one member forming sulfite from thiosulfate and another consuming it. Strain AHT17 formed an independent deep phylogenetic lineage within the Clostridiales and is proposed as a new genus and species Desulfitisporum alkaliphilum gen. nov., sp. nov. (=DSM 22410T = UNIQEM U794T). Electronic supplementary material The online version of this article (doi:10.1007/s00792-010-0310-y) contains supplementary material, which is available to authorized users.

Muyzer, Gerard

2010-01-01

382

'Candidatus Megaira polyxenophila' gen. nov., sp. nov.: Considerations on Evolutionary History, Host Range and Shift of Early Divergent Rickettsiae.  

PubMed

"Neglected Rickettsiaceae" (i.e. those harboured by non-hematophagous eukaryotic hosts) display greater phylogenetic variability and more widespread dispersal than pathogenic ones; yet, the knowledge about their actual host range and host shift mechanism is scarce. The present work reports the characterization following the full-cycle rRNA approach (SSU rRNA sequence, specific in situ hybridization, and ultrastructure) of a novel rickettsial bacterium, herewith proposed as 'Candidatus Megaira polyxenophila' gen. nov., sp. nov. We found it in association with four different free-living ciliates (Diophrys oligothrix, Euplotes octocarinatus, Paramecium caudatum, and Spirostomum sp., all belonging to Alveolata, Ciliophora); furthermore it was recently observed as intracellular occurring in Carteria cerasiformis and Pleodorina japonica (Chlorophyceae, Chlorophyta). Phylogenetic analyses demonstrated the belonging of the candidate new genus to the family Rickettsiaceae (Alphaproteobacteria, Rickettsiales) as a sister group of the genus Rickettsia. In situ observations revealed the ability of the candidate new species to colonize either nuclear or cytoplasmic compartments, depending on the host organism. The presence of the same bacterial species within different, evolutionary distant, hosts indicates that 'Candidatus Megaira polyxenophila' recently underwent several distinct host shifts, thus suggesting the existence of horizontal transmission pathways. We consider these findings as indicative of an unexpected spread of rickettsial infections in aquatic communities, possibly by means of trophic interactions, and hence propose a new interpretation of the origin and phylogenetic diversification of rickettsial bacteria. PMID:23977321

Schrallhammer, Martina; Ferrantini, Filippo; Vannini, Claudia; Galati, Stefano; Schweikert, Michael; Görtz, Hans-Dieter; Verni, Franco; Petroni, Giulio

2013-08-20

383

Modestobacter multiseptatus gen. nov., sp. nov., a budding actinomycete from soils of the Asgard Range (Transantarctic Mountains).  

PubMed

Oligotrophic PYGV medium, inoculated with soils from Linnaeus Terrace (1600 m, Antarctica), yielded four aerobic actinomycetes with short rods, multiple and irregular septa and often motile buds. Cells were 1.0-2.8 x 1.0-3.0 microm and colonies were beige to pink. The isolates were nearly identical in physiological and biochemical tests. Three strains grew from 0 degrees C to 25-28 degrees C, but one was psychrophilic with a maximum growth temperature of 20 degrees C. Carbon sources utilized were D-glucose, D-galactose, lactose, sucrose or mannitol; malate, succinate, fumarate, pyruvate or glutarate were decarboxylated aerobically. Peptone and yeast extract were the preferred nitrogen sources. Nitrate was reduced aerobically or anaerobically. Cell walls contained meso-diaminopimelic acid, glutamate, alanine, glycine, galactose, glucose and ribose. Major fatty acids of strains AA-802, -824, -825 and -826T were n18:1, i16:0 and ai17:0. Major respiratory quinones were MK-9(H4) and MK-8(H4). Polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol. Phosphatidylglycerol was found in most strains. The DNA G+C contents were 68-70 mol%. In 16S rDNA analyses, similarity values obtained for 500 nucleotides from the 5' terminus were > 99.5%. Almost complete sequences from AA-826T and -825 were 99.9% similar. Strain AA-826T belonged to a novel cluster of desert soil and rock isolates within the Geodermatophilaceae and was equidistantly related to members of Geodermatophilus and to a Blastococcus lineage. The four isolates represent a new genus, Modestobacter gen. nov., with Modestobacter multiseptatus sp. nov. as the type species. The type strain, Modestobacter multiseptatus AA-826T, was deposited in the DSMZ as DSM 44406T. PMID:10826821

Mevs, U; Stackebrandt, E; Schumann, P; Gallikowski, C A; Hirsch, P

2000-01-01

384

Zavarzinella formosa gen. nov., sp. nov., a novel stalked, Gemmata-like planctomycete from a Siberian peat bog.  

PubMed

An aerobic, pink-pigmented, budding and rosette-forming bacterium was isolated from an acidic Sphagnum peat bog and designated strain A10(T). The 16S rRNA gene sequence analysis showed that strain A10(T) was a member of the order Planctomycetales and belonged to a phylogenetic lineage defined by the genus Gemmata, with 90 % sequence similarity to that of Gemmata obscuriglobus, the only taxonomically described organism of this group. Ellipsoid-shaped cells of strain A10(T) were uniformly covered with crateriform pits and possessed long (up to 10-15 mum) and unusually thick (0.5-0.7 mum) stalks of a unique ultrastructure. Thin sections revealed a complex intracellular membrane system compartmentalizing the cells. Strain A10(T) was a moderately acidophilic, mesophilic organism capable of growth at pH values between 3.8 and 7.2 (with an optimum at pH 5.5-6.0) and at temperatures between 10 and 30 degrees C (with an optimum at 20-25 degrees C). The major fatty acids were C(18 : 0), C(18 : 1)omega5c and C(16 : 1)omega5c and the major quinone was MK-6. Cells of strain A10(T) contained high amounts of bound saturated and monounsaturated C(26)-C(32) (omega-1) hydroxy fatty acids. The G+C content of the DNA was 62.5 mol%. The unique cell morphology, the capability of growth in acidic conditions and a number of chemotaxonomic and genotypic characteristics served to differentiate strain A10(T) from G. obscuriglobus. Based on these data, the novel isolate should be considered as representing a novel genus and species of planctomycetes, for which the name Zavarzinella formosa gen. nov., sp. nov. is proposed The type strain is A10(T) (=DSM 19928(T)=VKM B-2478(T)). PMID:19196778

Kulichevskaya, Irina S; Baulina, Olga I; Bodelier, Paul L E; Rijpstra, W Irene C; Damsté, Jaap S Sinninghe; Dedysh, Svetlana N

2009-02-01

385

Methanolinea tarda gen. nov., sp. nov., a methane-producing archaeon isolated from a methanogenic digester sludge.  

PubMed

A novel methane-producing archaeon, strain NOBI-1(T) was isolated from an anaerobic, propionate-degradation enrichment culture, which was originally obtained from a mesophilic methanogenic sludge digesting municipal sewage sludge. Cells were non-motile, rod-shaped, 0.7-1.0 microm by 2.0 microm, and formed multicellular filaments longer than 8 microm. Growth was observed between 35 and 55 degrees C (optimum 50 degrees C) and pH 6.7 and 8.0 (optimum pH 7.0). The G+C content of the genomic DNA was 56.3 mol%. The strain utilized H(2) and formate for growth and methane production. Based on comparative sequence analyses of the 16S rRNA gene and mcrA gene (encoding the alpha subunit of methyl-coenzyme M reductase, a key enzyme in the methane-production pathway), strain NOBI-1(T) was affiliated with the order Methanomicrobiales, but it was significantly distant from any other known species within the order. The most closely related species based on 16S rRNA and mcrA gene sequence similarity were respectively 'Candidatus Methanoregula boonei' (93.7% 16S rRNA gene sequence similarity) and Methanocorpusculum parvum (74.2% deduced McrA amino acid sequence similarity to the type strain). These phenotypic and genetic properties justified the creation of a novel species of a new genus for the strain, for which we propose the name Methanolinea tarda gen. nov., sp. nov. The type strain of Methanolinea tarda is strain NOBI-1(T) (=DSM 16494(T) =JCM 12467(T) =NBRC 102358(T)). PMID:18175725

Imachi, Hiroyuki; Sakai, Sanae; Sekiguchi, Yuji; Hanada, Satoshi; Kamagata, Yoichi; Ohashi, Akiyoshi; Harada, Hideki

2008-01-01

386

Alpinimonas psychrophila gen. nov., sp. nov., an actinobacterium of the family Microbacteriaceae isolated from alpine glacier cryoconite.  

PubMed

A Gram-type positive, Gram-reaction variable, non-motile, psychrophilic actinobacterium, designated Cr8-25(T), was isolated from alpine glacier cryoconite and was able to grow well over a temperature range of 1-15 °C. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain Cr8-25(T) belonged to the family Microbacteriaceae and showed highest 16S rRNA gene sequence similarity with Klugiella xanthotipulae 44C3(T) (97.0%). However, strain Cr8-25(T) could be differentiated from the type strain of K. xanthotipulae on the level of genomospecies by a DNA-DNA relatedness value of only 37.2%. Strain Cr8-25(T) contained a cell-wall peptidoglycan that was cross-linked according to the B-type, which is based on 2,4-diaminobutyric acid. The cell wall contained the sugars galactose, fucose and rhamnose. The predominant cellular fatty acids of strain Cr8-25(T) were C(15:0) anteiso (64.6%) and iso-C(16:0) (22.5%) and the major menaquinones were MK-11 and MK-10. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and unknown glycolipids. The G+C content of the genomic DNA was 58.8 mol%. On the basis of the phenotypic characteristics, phylogenetic and chemotaxonomic analyses and DNA-DNA relatedness data, strain Cr8-25(T) represents a novel species of a new genus in the family Microbacteriaceae, for which the name Alpinimonas psychrophila gen. nov., sp. nov. is proposed. The type strain is Cr8-25(T) (=DSM 23737(T)=LMG 26215(T)). PMID:22228665

Schumann, Peter; Zhang, De-Chao; Redzic, Mersiha; Margesin, Rosa

2012-01-06

387

Glaciimonas immobilis gen. nov., sp. nov., a member of the family Oxalobacteraceae isolated from alpine glacier cryoconite.  

PubMed

Strains Cr9-30(T) and Cr9-12 were isolated from alpine glacier cryoconite. Both strains were Gram-negative-staining, non-motile, rod-shaped and psychrophilic, showing good growth over the temperature range 1-20 °C. Phylogenetic analysis of 16S rRNA gene sequences revealed that the two strains formed a distinct branch within the family Oxalobacteraceae and were most closely related to members of the genus Collimonas. The 16S rRNA gene sequence similarity between strains Cr9-30(T) and Cr9-12 was 99.0?%. The two strains showed highest 16S rRNA gene sequence pairwise similarity with Collimonas pratensis LMG 23965(T) (96.6 and 96.1?% for strains Cr9-30(T) and Cr9-12, respectively), Collimonas arenae LMG 23964(T) (96.5 and 96.3?%, respectively) and Collimonas fungivorans LMG 21973(T) (96.4 and 96.2?%, respectively). The predominant cellular fatty acids were summed feature 3 (C??:??7c and/or iso-C??:? 2-OH), C??:? and C??:??7c. The DNA G+C content of strain Cr9-30(T) was 51.0 mol%. On the basis of phenotypic characteristics and phylogenetic analysis, strains Cr9-30(T) and Cr9-12 represent a novel species in a new genus of the family Oxalobacteraceae, for which the name Glaciimonas immobilis gen. nov., sp. nov. is proposed. The type strain of Glaciimonas immobilis is Cr9-30(T) (?=?DSM 23240(T)?=?LMG 25547(T)). PMID:20935085

Zhang, De-Chao; Redzic, Mersiha; Schinner, Franz; Margesin, Rosa

2010-10-08

388

Litoricolaceae fam. nov., to include Litoricola lipolytica gen. nov., sp. nov., a marine bacterium belonging to the order Oceanospirillales.  

PubMed

A Gram-negative, non-motile, chemoheterotrophic, facultatively aerobic, short-rod-shaped bacterium, designated IMCC1097(T), was isolated from coastal seawater (10 m depth) of the East Sea, Korea. The temperature, pH and NaCl ranges for growth were 15-30 degrees C, pH 5.0-10.0 and 1.5-10 % NaCl. The colonies of the strain were very small, having a mean diameter of 0.05 mm. 16S rRNA gene sequence data indicated that the strain was most closely related to genera within the class Gammaproteobacteria. Members of the most closely related genera showed less than 90 % sequence similarity and included Saccharospirillum (89.3 %), Oleiphilus (88.7 %), Reinekea (88.2 %), Alcanivorax (86.4-87.6 %) and Zooshikella (87.6 %), which represent five different families of the order Oceanospirillales. Phylogenetic analyses showed that this marine strain represented a distinct phylogenetic lineage in the order Oceanospirillales and could not be assigned to any of the defined families in the order. The predominant fatty acids were C(16 : 1) omega 7c and/or iso-C(15 : 0) 2-OH, C(18 : 1) omega 7c and C(10 : 0) 3-OH, and the DNA G+C content was 57.9 mol%. These chemotaxonomic properties, together with phenotypic characteristics, served to differentiate the strain from phylogenetically closely related genera. The very low sequence similarities (<90 %) and distant relationships between IMCC1097(T) and members of the order Oceanospirillales suggested that the strain merited classification within a novel genus within a novel family in the order. On the basis of taxonomic evidence collected in this study, a novel genus and species are proposed, Litoricola lipolytica gen. nov., sp. nov., within a new family Litoricolaceae fam. nov. Strain IMCC1097(T) (=KCCM 42360(T) =NBRC 102074(T)) is the type strain of Litoricola lipolytica. PMID:17684259

Kim, Hana; Choo, Yoe-Jin; Cho, Jang-Cheon

2007-08-01

389

Sungkyunkwania multivorans gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from seawater from a seaweed farm.  

PubMed

A Gram-staining-negative, non-flagellated, non-gliding and rod-shaped bacterial strain, designated PDB-16(T), was isolated from seawater from a seaweed farm on the South Sea in Korea, and its taxonomic position was investigated using a polyphasic approach. Strain PDB-16(T) grew optimally at 30 °C, at pH 7.0-7.5 and in the presence of 2% (w/v) NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences revealed that strain PDB-16(T) formed an independent lineage within the evolutionary radiation encompassed by the family Flavobacteriaceae. Strain PDB-16(T) contained MK-6 as the predominant menaquinone and iso-C15:0, iso-C15:1 G and iso-C17:0 3-OH as the major fatty acids. The major polar lipids detected in strain PDB-16(T) were phosphatidylethanolamine and two unidentified lipids. The DNA G+C content of strain PDB-16(T) was 42.1 mol%. Strain PDB-16(T) exhibited very low 16S rRNA gene sequence similarities of less than 89.7% to the type strains of any bacterial species with validly published names and less than 90.1% to uncultured bacteria clones. The 16S rRNA gene sequence similarity values and the differences in phenotypic properties between strain PDB-16(T) and some phylogenetically related genera were sufficient to support the proposal that strain PDB-16(T) should be distinguished from previously known genera of the family Flavobacteriaceae. On the basis of the data presented, strain PDB-16(T) is considered to represent a new genus and novel species, for which the name Sungkyunkwania multivorans gen. nov., sp. nov. is proposed. The type strain of Sungkyunkwania multivorans is PDB-16(T) (=KCTC 32138(T)=CCUG 62952(T)). PMID:23041634

Yoon, Jung-Hoon; Gyeong, Hye Ryeon; Kim, Soo-In

2012-10-05

390

Magnetospira thiophila gen. nov., sp. nov., a marine magnetotactic bacterium that represents a novel lineage within the Rhodospirillaceae (Alphaproteobacteria).  

PubMed

A marine, magnetotactic bacterium, designated strain MMS-1(T), was isolated from mud and water from a salt marsh in Woods Hole, Massachusetts, USA, after enrichment in defined oxygen-concentration/redox-gradient medium. Strain MMS-1(T) is an obligate microaerophile capable of chemoorganoheterotrophic and chemolithoautotrophic growth. Optimal growth occurred at pH 7.0 and 24-26 °C. Chemolithoautotrophic growth occurred with thiosulfate as the electron donor and autotrophic carbon fixation was via the Calvin-Benson-Bassham cycle. The G+C content of the DNA of strain MMS-1(T) was 47.2 mol%. Cells were Gram-negative and morphologically variable, with shapes that ranged from that of a lima bean to fully helical. Cells were motile by means of a single flagellum at each end of the cell (amphitrichous). Regardless of whether grown in liquid or semi-solid cultures, strain MMS-1(T) displayed only polar magnetotaxis and possessed a single chain of magnetosomes containing elongated octahedral crystals of magnetite, positioned along the long axis of the cell. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain MMS-1(T) belongs to the family Rhodospirillaceae within the Alphaproteobacteria, and is distantly related to species of the genus Magnetospirillum. Strain MMS-1(T) is therefore considered to represent a novel species of a new genus, for which the name Magnetospira thiophila gen. nov., sp. nov. is proposed. The type strain of Magnetospira thiophila is MMS-1(T) (?=?ATCC BAA-1438(T)?=?JCM 17960(T)). PMID:22140150

Williams, Timothy J; Lefèvre, Christopher T; Zhao, Weidong; Beveridge, Terry J; Bazylinski, Dennis A

2011-11-25

391

Lutibacter litoralis gen. nov., sp. nov., a marine bacterium of the family Flavobacteriaceae isolated from tidal flat sediment.  

PubMed

A rod-shaped marine bacterium, designated strain CL-TF09T, isolated from a tidal flat in Ganghwa, Korea, was characterized based on its physiological and biochemical features, fatty acid profile and phylogenetic position. 16S rRNA gene sequence analysis revealed a clear affiliation with the family Flavobacteriaceae. Strain CL-TF09T showed the closest phylogenetic relationship with the genera Tenacibaculum and Polaribacter; sequence similarities between CL-TF09T and the type strains of Tenacibaculum and Polaribacter species ranged from 90.7 to 91.8 %. Cells of strain CL-TF09T were non-motile and grew on solid media as yellow colonies. The strain grew in the presence of 1-5 % sea salts, within a temperature range of 5-30 degrees C and at pH 7-8. The strain had iso-C(15 : 0) 3-OH (17.4 %), iso-C(15 : 0) (16.7 %), anteiso-C(15 : 0) (15.1 %) and iso-C(16 : 0) 3-OH (13.4 %) as predominant fatty acids. The DNA G+C content was 33.9 mol%. Based on the physiological, fatty acid composition and phylogenetic data presented, strain CL-TF09T is considered to represent a novel genus and species of the family Flavobacteriaceae, for which the name Lutibacter litoralis gen. nov., sp. nov. is proposed. The type strain is CL-TF09T (=KCCM 42118T = JCM 13034T). PMID:16585692

Choi, Dong H; Cho, Byung C

2006-04-01

392

Frischella perrara gen. nov., sp. nov., a gammaproteobacterium isolated from the gut of the honeybee, Apis mellifera.  

PubMed

The gut of the Western honeybee, Apis mellifera, is colonized by a characteristic set of bacteria. Two distinct gammaproteobacteria are consistent members of this unique microbial community, and one has recently been described in a new genus and species with the name Gilliamella apicola. Here, we present the isolation and characterization of PEB0191(T), a strain belonging to the second gammaproteobacterial species present in the honeybee gut microbiota, formerly referred to as 'Gammaproteobacterium-2'. Cells of strain PEB0191(T) were mesophilic and had a mean length of around 2 µm, and optimal growth was achieved under anaerobic conditions. Growth was not obtained under aerobic conditions and was reduced in a microaerophilic environment. Based on 16S rRNA gene sequence analysis, strain PEB0191(T) belongs to the family Orbaceae, and its closest relatives, with around 95?% sequence similarity, are species of the genera Orbus and Gilliamella. Phylogenetic analyses suggest that PEB0191(T) is more closely related to the genus Orbus than to the genus Gilliamella. In accordance with its evolutionary relationship, further similarities between strain PEB0191(T) and other members of the family Orbaceae were revealed based on the respiratory quinone type (ubiquinone 8), the fatty acid profile and the DNA G+C content. Interestingly, like strains of the genus Gilliamella, PEB0191(T) exhibited a high level of resistance to oxytetracycline. The similar levels of sequence divergence from the genera Gilliamella and Orbus and its uncertain phylogenetic position within the family Orbaceae indicate that strain PEB0191(T) represents a novel species of a new genus, with the proposed name Frischella perrara gen. nov., sp. nov. The type strain of Frischella perrara is PEB0191(T) (?=?NCIMB 14821(T)?=?ATCC BAA-2450(T)). PMID:23606484

Engel, Philipp; Kwong, Waldan K; Moran, Nancy A

2013-04-19

393

Spongiibacter marinus gen. nov., sp. nov., a halophilic marine bacterium isolated from the boreal sponge Haliclona sp. 1.  

PubMed

Strain HAL40b(T) was isolated from the marine sponge Haliclona sp. 1 collected at the Sula Ridge off the Norwegian coast and characterized by physiological, biochemical and phylogenetic analyses. The isolate was a small rod with a polar flagellum. It was aerobic, Gram-negative and oxidase- and catalase-positive. Optimal growth was observed at 20-30 degrees C, pH 7-9 and in 3 % NaCl. Substrate utilization tests were positive for arabinose, Tween 40 and Tween 80. Enzyme tests were positive for alkaline phosphatase, esterase lipase (C8), leucine arylamidase, acid phosphatase, naphthol-AS-BI-phosphohydrolase and N-acetyl-beta-glucosaminidase. The predominant cellular fatty acid was C(17 : 1) omega8, followed by C(17 : 0) and C(18 : 1) omega7. Analysis by matrix-assisted laser desorption/ionization time-of-flight MS was used to characterize the strain, producing a characteristic low-molecular-mass protein pattern that could be used as a fingerprint for identification of members of this species. The DNA G+C content was 69.1 mol%. Phylogenetic analysis supported by 16S rRNA gene sequence comparison classified the strain as a member of the class Gammaproteobacteria. Strain HAL40b(T) was only distantly related to other marine bacteria including Neptunomonas naphthovorans and Marinobacter daepoensis (type strain sequence similarity >90 %). Based on its phenotypic, physiological and phylogenetic characteristics, it is proposed that the strain should be placed into a new genus as a representative of a novel species, Spongiibacter marinus gen. nov., sp. nov.; the type strain of Spongiibacter marinus is HAL40b(T) (=DSM 17750(T) =CCUG 54896(T)). PMID:18319460

Graeber, Ingeborg; Kaesler, Ines; Borchert, Martin S; Dieckmann, Ralf; Pape, Thomas; Lurz, Rudi; Nielsen, Preben; von Döhren, Hans; Michaelis, Walter; Szewzyk, Ulrich

2008-03-01

394

Anditalea andensis gen. nov., sp. nov., an alkaliphilic, halotolerant bacterium isolated from extreme alkali-saline soil.  

PubMed

A novel alkalophilic salt-tolerant rod-shaped bacterium, designated ANESC-S(T), was isolated from an extremely alkali-saline soil in the rural area of Anda city in northeast China. Taxonomic study using a polyphasic approach revealed that this non-motile, orange colony-forming microbe was Gram-negative and obligately aerobic. Optimal growth of strain ANESC-S(T) was achieved in the presence of NaCl with a concentration range of 0.5 to 4 % and pH between 7.5 and 9.2, and at temperatures ranging from 10 to 37 °C. Phylogenetic analysis of 16S rRNA sequences showed that of strain ANESC-S(T) is most homologous to Mongoliicoccus roseus MIM28(T) and Litoribacter ruber YIM CH208(T) with sequence similarity of 95.1 and 93.2 %, respectively. The genomic DNA G+C content of strain ANESC-S(T) was determined to be 39.1 mol%. The main isoprenoid quinone in ANESC-S(T) was found to be menaquinone-7. The main fatty acids were found to be iso-C(15:0) (27.5 %), iso-C(17:0)3-OH (14.0 %), anteiso-C(15:0) (9.8 %), summed feature 9 (iso-C(17:1)?9c and/or 10-methyl C(16:0) 10.6 %) and summed feature 3 (C(16:1)w7c/C(16:1)w6c, 9.78 %). Based on the phenotypic, chemotaxonomic and phylogenetic data, strain ANESC-S(T) is considered to represent a new genus and species classified into the order Cytophagales, for which the name Anditalea andensis gen. nov., sp. nov. is proposed. The type strain is ANESC-S(T) (=CICC 10485(T) = NCCB 100412(T)). PMID:22772978

Shi, Wei; Takano, Tetsuo; Liu, Shenkui

2012-07-08

395

Geosporobacter subterraneus gen. nov., sp. nov., a spore-forming bacterium isolated from a deep subsurface aquifer.  

PubMed

A novel, strictly anaerobic, chemo-organotrophic bacterium, designated strain VNs68(T), was isolated from a well that collected water from a deep aquifer at a depth of 800 m in the Paris Basin, France. Cells were thin, non-motile, Gram-positive rods forming terminal endospores (3.0-5.0 x 0.5 microm). Strain VNs68(T) grew at temperatures between 30 and 55 degrees C (optimum 42 degrees C) and at pH 5.6-8.4 (optimum pH 7.3). It did not require salt for growth but tolerated up to 40 g NaCl l(-1). Strain VNs68(T) was an obligate heterotroph fermenting carbohydrates such as glucose, xylose, fructose, ribose and cellobiose. Casamino acids and amino acids (arginine, serine, lysine, alanine, aspartate, asparagine, isoleucine, histidine) were also fermented. The main fermentation products from glucose were acetate with H(2) and CO(2). Sulfate, sulfite, thiosulfate, elemental sulfur, nitrate and nitrite were not used as electron acceptors. The G+C content of the genomic DNA was 42.2 mol%. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain VNs68(T) was affiliated to cluster XI, order Clostridiales, domain Bacteria. On the basis of 16S rRNA gene sequence comparisons and physiological characteristics, strain VNs68(T) is considered to represent a novel species of a new genus, for which the name Geosporobacter subterraneus gen. nov., sp. nov. is proposed. The type strain of Geosporobacter subterraneus is VNs68(T) (=DSM 17957(T) =JCM 14037(T)). PMID:17684251

Klouche, Nihel; Fardeau, Marie-Laure; Lascourrèges, Jean-François; Cayol, Jean-Luc; Hacene, Hocine; Thomas, Pierre; Magot, Michel

2007-08-01

396

Thermoterrabacterium ferrireducens gen. nov., sp. nov., a thermophilic anaerobic dissimilatory Fe(III)-reducing bacterium from a continental hot spring  

SciTech Connect

A strain of a thermophilic, anaerobic, dissimilatory, Fe(III)-reducing bacterium, Thermoterrabacterium ferrireducens gen. nov., sp. nov. (type strain JW/AS-Y7{sup T}; DSM 11255), was isolated from hot springs in Yellowstone National Park and New Zealand. The gram-positive-staining cells occurred singly or in pairs as straight to slightly curved rods, 0.3 to 0.4 by 1.6 to 2.7 {mu}m, with rounded ends and exhibited a tumbling motility. Spores were not observed. The temperature range for growth was 50 to 74{degrees}C with an optimum at 65{degrees}C. The pH range for growth at 65{degrees}C was from 5.5 to 7.6, with an optimum at 6.0 to 6.2. The organism coupled the oxidation of glycerol to reduction of amorphous Fe(III) oxide or Fe(III) citrate as an electron acceptor. In the presence as well as in the absence of Fe(III) and in the presence of CO{sub 2}, glycerol was metabolized by incomplete oxidation to acetate as the only organic metabolic product; no H{sub 2} was produced during growth. The organism utilized glycerol, lactate, 1,2-propanediol, glycerate, pyruvate, glucose, fructose, mannose, and yeast extract as substrates. In the presence of Fe(III) the bacterium utilized molecular hydrogen. The organism reduced 9,10-anthraquinone-2,6-disulfonic acid, fumarate (to succinate), and thiosulfate (to elemental sulfur) but did not reduce MnO{sub 2}, nitrate, sulfate, sulfite, or elemental sulfur. The G+C content of the DNA was 41 mol% (as determined by high-performance liquid chromatography). The 16S ribosomal DNA sequence analysis placed the isolated strain as a member of a new genus within the gram-type positive Bacillus-Clostridium subphylum.

Slobodkin, A.; Wiegel, J. [Univ. of Georgia, Athens, GA (United States); Reysenbach, A.L. [Rutgers Univ., New Brunswick, NJ (United States)] [and others

1997-04-01

397

Halomicroarcula pellucida gen. nov., sp. nov., a non-pigmented, transparent-colony-forming, halophilic archaeon isolated from solar salt.  

PubMed

A novel halophilic strain, BNERC31(T), was isolated from solar salt, 'Sel marin de Guérande', imported from France. Colonies on agar medium containing soluble starch, sodium citrate, sodium glutamate and inorganic salts were non-pigmented and transparent, while cells obtained by centrifuging liquid cultures were red-pigmented. Cells of strain BNERC31(T) were non-motile, pleomorphic, stained Gram-negative and lysed in distilled water. Growth occurred with 20-30?% (w/v) NaCl (optimum, 25?%, w/v), with 0-500 mM MgCl2 (optimum, 10 mM), at pH 6.0-8.5 (optimum, pH 7.0) and at 25-55 °C (optimum, 40 °C). Growth was dependent on soluble starch, and inhibited completely by 0.5?% organic nutrients, such as Casamino acids or yeast extract. The DNA G+C content was 64.1 mol%. Strain BNERC31(T) possessed at least two heterogeneous 16S rRNA genes, and the sequence of the orthologous gene (preceded by the dihydroorotate oxidase gene, pyrD) showed the highest similarity (96.5?%) to that of Haloarcula marismortui JCM 8966(T). The RNA polymerase subunit B' gene sequence showed the highest similarity (91.7?%) to that of Haloarcula amylolytica JCM 13557(T). The polar lipids of strain BNERC31(T) were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate, diglycosyl diether and sulfated diglycosyl diether, similar to those of species of the genus Halomicrobium. The phenotypic and phylogenetic characteristics showed that strain BNERC31(T) differed from species of the genera Haloarcula and Halomicrobium and indicated that it represents a novel species in a new genus, for which the name Halomicroarcula pellucida gen. nov., sp. nov. is proposed. The type strain of the type species is BNERC31(T) (?=?JCM 17820(T)?=?CECT 7537(T)). PMID:23563231

Echigo, Akinobu; Minegishi, Hiroaki; Shimane, Yasuhiro; Kamekura, Masahiro; Itoh, Takashi; Usami, Ron

2013-04-05

398

Leptobacterium flavescens gen. nov., sp. nov., a marine member of the family Flavobacteriaceae, isolated from marine sponge and seawater.  

PubMed

Six obligately aerobic, Gram-negative, non-motile, pale-yellow-pigmented, rod-shaped bacterial strains, designated YM3-301(T), HG868, 04PA2 Co4-8B, 04PA2 Co4-99A, 04PA2 018SW-3 and 04PA2 018SW-18, were isolated from a marine sponge and seawater and were subjected to a polyphasic taxonomic investigation. Phylogenetic analyses based on 16S rRNA gene sequences revealed that the novel isolates were affiliated with the family Flavobacteriaceae (phylum Bacteroidetes) and that they showed the highest sequence similarity (90.3-90.9 %) to members of the genus Leeuwenhoekiella and to Zhouia amylotica. The 16S rRNA gene sequence similarities with respect to members of other related genera were only 86.3-89.1 %. In contrast, the six isolates shared high levels of 16S rRNA gene sequence similarity (99.7-100 %) and DNA-DNA relatedness (72-94 %) with each other. The novel isolates were phenotypically and physiologically different from members of related genera. The G+C content of the DNA was 41.8-43.5 mol%, MK-6 was the major menaquinone and i15 : 0, i15 : 1 and i17 : 0 3-OH were the major fatty acids. On the basis of the data from the taxonomic studies, it was concluded that these six novel strains represent a novel genus and species of the family Flavobacteriaceae, for which the name Leptobacterium flavescens gen. nov., sp. nov. is proposed. The type strain of Leptobacterium flavescens is YM3-301(T) (=KCTC 22160(T)=MBIC 06275(T)=NBRC 104141(T)). PMID:19196755

Mitra, Sharbanee; Matsuo, Yoshihide; Haga, Tomomi; Yasumoto-Hirose, Mina; Yoon, Jaewoo; Kasai, Hiroaki; Yokota, Akira

2009-02-01

399

Huanghella arctica gen. nov., sp. nov., a bacterium of the family Cytophagaceae isolated from Arctic tundra soil.  

PubMed

A novel, strictly aerobic, red-pigmented, gram-reaction-negative bacterium, designated strain R9-9(T), was isolated from tundra soil collected near Ny-Ålesund, Svalbard Archipelago, Norway (78° N). The novel strain was subjected to a taxonomic study using a polyphasic approach. It grew optimally at 20-22 °C and at pH 7.0. Flexirubin-type pigments were absent. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain R9-9(T) represents a distinct phyletic line that reflects a novel generic status within the family Cytophagaceae. The novel strain showed relatively low 16S rRNA gene sequence similarities (<88.0?%) to members of established genera. Strain R9-9(T) contained summed feature 3 (C(16?:?1)?7c and/or C(16?:?1)?6c), iso-C(17?:?0) 3-OH, iso-C(15?:?0) and C(16?:?1)?5c as its major cellular fatty acids, phosphatidylethanolamine as its main polar lipid, and MK-7 as its major respiratory quinone. The genomic DNA G+C content was 56.1 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain R9-9(T) is considered to represent a novel species in a new genus in the family Cytophagaceae, for which the name Huanghella arctica gen. nov., sp. nov. is proposed. The type strain is R9-9(T) (?=?CCTCC AB 2010418(T)?=?NRRL B-59750(T)). PMID:22544798

Jiang, Fan; Xiao, Mengchen; Chen, Lu; Kan, Wenjing; Peng, Fang; Dai, Jun; Chang, Xulu; Li, Wenxin; Fang, Chengxiang

2012-04-27

400

Thiohalobacter thiocyanaticus gen. nov., sp. nov., a moderately halophilic, sulfur-oxidizing gammaproteobacterium from hypersaline lakes, that utilizes thiocyanate.  

PubMed

A moderately halophilic, obligately chemolithoautotrophic, sulfur-oxidizing bacterium, designated strain HRh1(T), was obtained from mixed sediment samples from hypersaline chloride-sulfate lakes in the Kulunda Steppe, in south-western Siberia (Russia), using aerobic enrichment culture at 1 M NaCl with thiocyanate as substrate. Cells of the isolate were short, non-motile rods with a Gram-negative type of cell wall. The bacterium was an obligate aerobe capable of chemolithoautotrophic growth with thiocyanate and thiosulfate. With thiosulfate, it grew at NaCl concentrations of 0.2-3.0 M (optimum 0.5 M) and at pH 6.3-8.0 (optimum pH 7.3-7.5). During growth on thiocyanate, cyanate was identified as an intermediate. The dominant cellular fatty acids were C(16 : 0) and C(18 : 1)omega7. Phylogenetic analysis based on 16S rRNA gene sequencing placed the isolate in the class Gammaproteobacteria as an independent lineage, with an unclassified marine sulfur-oxidizing bacterium as the closest culturable relative (93 % sequence similarity). A single cbbL gene (coding for the key enzyme of the Calvin-Benson cycle of autotrophic CO(2) assimilation) with relatively low similarity to any homologous genes found in chemolithoautotrophs was detected in strain HRh1(T). On the basis of our phenotypic and phylogenetic analysis, the halophilic isolate is proposed to represent a new genus and novel species, Thiohalobacter thiocyanaticus gen. nov., sp. nov. The type strain of Thiohalobacter thiocyanaticus is HRh1(T) (=DSM 21152(T) =UNIQEM U249(T)). PMID:19654366

Sorokin, Dimitry Yu; Kovaleva, Olga L; Tourova, Tatjana P; Muyzer, Gerard

2009-08-04

401

Thermophagus xiamenensis gen. nov., sp. nov., a moderately thermophilic and strictly anaerobic bacterium isolated from hot spring sediment.  

PubMed

A moderately thermophilic and strictly anaerobic bacterium, designated HS1(T), was isolated from offshore hot spring sediment in Xiamen, China. Cells were Gram-negative, catalase-positive, oxidase-negative, slender and flexible rods without flagella. The strain could grow at 35-55 °C (optimum at 50 °C) and in 1-8 % NaCl (w/v; optimum 2-4 %). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain HS1(T) was affiliated with the family Marinilabiliaceae and shared a distant relationship with the previously described genera. The isolate was most closely related to Anaerophaga thermohalophila Fru22(T) with 16S rRNA gene sequence similarity of 92.4 %, followed by the other members of the family Marinilabiliaceae with 88.7-91.1 % similarity. The dominant cellular fatty acids were iso-C(15 : 0) and anteiso-C(15 : 0). The predominant quinone was MK-7. The major polar lipids were phosphatidylethanolamine (PE) and an unknown polar lipid. The genomic DNA G+C content was 38.7 mol%. Besides the phylogenetically distant relationship, strain HS1(T) was obviously distinguished from the most closely related genera in several phenotypic properties including colony colour and pigment production, optimal temperature, optimal NaCl, relation to O(2), bicarbonate/carbonate requirement, catalase activity, nitrate reduction, fermentation products and cellular fatty acid profile. Based on the phenotypic and phylogenetic data, strain HS1(T) represents a novel species of a new genus, for which the name Thermophagus xiamenensis gen. nov., sp. nov. is proposed. The type strain of the type species is HS1(T) (= DSM 19012(T) = CGMCCC 1.5071(T)). PMID:22345138

Gao, Zhao-Ming; Liu, Xin; Zhang, Xi-Ying; Ruan, Ling-Wei

2012-02-17

402

Aciditerrimonas ferrireducens gen. nov., sp. nov., an iron-reducing thermoacidophilic actinobacterium isolated from a solfataric field.  

PubMed

An iron-reducing, moderately thermophilic, acidophilic actinobacterium, strain IC-180(T), isolated from a solfataric field in Hakone, Japan, was subjected to polyphasic taxonomic analysis. Strain IC-180(T) was a motile, short rod-shaped, Gram-positive bacterium that was able to grow at temperatures of 35-58 °C (optimally at 50 °C) and at pH 2.0-4.5 (optimally at pH 3.0). The strain grew aerobically and heterotrophically. It also grew anaerobically or autotrophically by dissimilatory reduction of ferric iron. No oxidation of ferrous iron was observed. Major cellular fatty acids detected were iso-C(16 : 0), anteiso-C(17 : 0) and iso-C(18 : 0); the major menaquinone was MK-9(H(8)). Phosphatidyl-N-methylethanolamine and an unknown ninhydrin-positive phosphoglycolipid were detected. The total DNA G+C content was 74.1 mol%. 16S rRNA gene sequence comparisons revealed that strain IC-180(T) was a member of the order Acidimicrobiales and clustered coherently with uncultured actinobacteria from a geothermal site and a bioreactor operated under moderately thermophilic conditions. This cluster could be distinguished from the two other clusters comprising the families of this order, Acidimicrobiaceae and Iamiaceae, respectively. Based on the properties of strain IC-180(T) determined in this polyphasic taxonomic study, this strain represents a novel species in a new genus in the order Acidimicrobiales, for which the name Aciditerrimonas ferrireducens gen. nov., sp. nov. is proposed; the type strain is IC-180(T) (?= JCM 15389(T) ?= DSM 45281(T)). PMID:20639230

Itoh, Takashi; Yamanoi, Kaoru; Kudo, Takuji; Ohkuma, Moriya; Takashina, Tomonori

2010-07-16

403

Halopelagius inordinatus gen. nov., sp. nov., a new member of the family Halobacteriaceae isolated from a marine solar saltern.  

PubMed

Two extremely halophilic archaea, strains RO5-2(T) and RO5-14, were isolated from Rudong marine solar saltern in Jiangsu, China. Cells of the two strains were pleomorphic, motile and stained Gram-negative. Colonies were red-pigmented. Strains RO5-2(T) and RO5-14 were able to grow at 20-50 degrees C (optimum 37 degrees C), at 2.6-4.8 M NaCl (optimum 3.4-3.9 M NaCl), at 0.03-0.7 M MgCl(2) (optimum 0.5 M MgCl(2)) and at pH 5.5-8.0 (optimum pH 6.5-7.0). Cells lyse in distilled water and the minimal NaCl concentration to prevent cell lysis was 12 % (w/v). The major polar lipids of the two strains were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and two major glycolipids chromatographically identical to sulfated mannosyl glucosyl diether (S-DGD-1) and mannosyl glucosyl diether (DGD-1). The 16S rRNA gene sequences of strains RO5-2(T) and RO5-14 showed 93.4-93.8 % similarity to the closest cultivated relative, Halosarcina pallida. The DNA G+C content of strains RO5-2(T) and RO5-14 was 61.0 mol% and 59.9 mol%, respectively. The DNA-DNA relatedness between strains RO5-2(T) and RO5-14 was 86.0 %. The phenotypic, chemotaxonomic and phylogenetic properties suggest that strains RO5-2(T) and RO5-14 represent a novel species in a new genus within the family Halobacteriaceae, for which the name Halopelagius inordinatus gen. nov., sp. nov. is proposed. The type strain is RO5-2(T) (=CGMCC 1.7739(T) =JCM 15773(T)). PMID:19854878

Cui, Heng-Lin; Li, Xin-Yi; Gao, Xia; Xu, Xue-Wei; Zhou, Yu-Guang; Liu, Hong-Can; Oren, Aharon; Zhou, Pei-Jin

2009-10-23

404

Salinarchaeum laminariae gen. nov., sp. nov.: a new member of the family Halobacteriaceae isolated from salted brown alga Laminaria.  

PubMed

Halophilic archaeal strains R26(T) and R22 were isolated from the brown alga Laminaria produced at Dalian, Liaoning Province, China. Cells from the two strains were pleomorphic rods and Gram negative, and colonies were red pigmented. Strains R26(T) and R22 were able to grow at 20-50°C (optimum 37°C) in 1.4-5.1 M NaCl (optimum 3.1-4.3 M) at pH 5.5-9.5 (optimum pH 8.0-8.5) and neither strain required Mg(2+) for growth. Cells lyse in distilled water and the minimum NaCl concentration required to prevent cell lysis was 8% (w/v) for strain R26(T) and 12% (w/v) for strain R22. The major polar lipids of the two strains were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and minor phosphatidylglycerol sulfate; glycolipids were not detected. Phylogenetic analyses based on 16S rRNA genes and rpoB' genes revealed that strains R26(T) and R22 formed a distinct clade with the closest relative, Natronoarchaeum mannanilyticum. The DNA G+C content of strains R26(T) and R22 was 65.8 and 66.4 mol%, respectively. The DNA-DNA hybridization value between strains R26(T) and R22 was 89%. The phenotypic, chemotaxonomic and phylogenetic properties suggest that the strains R26(T) and R22 represent a novel species in a new genus within the family Halobacteriaceae, for which the name Salinarchaeum laminariae gen. nov., sp. nov. is proposed. The type strain is R26(T) (type strain R26(T) = CGMCC 1.10590(T) = JCM 17267(T), reference strain R22 = CGMCC 1.10589). PMID:21901373

Cui, Heng-Lin; Yang, Xin; Mou, Yun-Zhuang

2011-09-08

405

Fluviimonas pallidilutea gen. nov., sp. nov., a new member of the family Cytophagaceae isolated from a freshwater river.  

PubMed

A bacterial strain designated TQQ6(T) was isolated from a freshwater river in Taiwan and characterized using a polyphasic taxonomy approach. Cells of strain TQQ6(T) were strictly aerobic, Gram-staining-negative, poly-?-hydroxybutyrate-containing, non-motile, non-spore-forming, long rods surrounded by a thick capsule and forming pale orange colonies. Growth occurred at 20-40 °C (optimum, 25 °C), at pH 7.0-9.0 (optimum, pH 8.0) and with 0-0.5?% NaCl (optimum, 0?%). The predominant fatty acids were iso-C15?:?0, summed feature 3 (comprising C16?:?1?6c and/or C16?:?1?7c), iso-C17?:?0 3-OH, C16?:?1?5c and C16?:?0. The major isoprenoid quinone was MK-7 and the DNA G+C content was 42.2 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylcholine, two uncharacterized aminophospholipids and three uncharacterized phospholipids. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain TQQ6(T) represents a distinct phyletic line that reflects a novel generic status within the family Cytophagaceae with relatively low sequence similarities (less than 90?%) to members of other genera with validly published names. On the basis of the genotypic and phenotypic data, strain TQQ6(T) represents a new genus and novel species of the family Cytophagaceae, for which the name Fluviimonas pallidilutea gen. nov., sp. nov. is proposed. The type strain is TQQ6(T) (?=?BCRC 80447(T)?=?LMG 27056(T)?=?KCTC 32035(T)). PMID:23687060

Sheu, Shih-Yi; Chen, Yu-Siang; Shiau, Yu-Wen; Chen, Wen-Ming

2013-05-17

406

Pustulibacterium marinum gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from the Bashi Channel.  

PubMed

A Gram-reaction-negative, non-spore-forming, gliding, non-translucent, colourless or yellow, aerobic and elevated-colony-forming strain, designated E403(T), was isolated from the Bashi Channel and subjected to a polyphasic taxonomic study. Strain E403(T) could grow in the presence of 0.3-8 % (w/v) NaCl, at 16-43 °C and at pH 6-9, and grew optimally at 28 °C, pH 8, in natural seawater medium. The respiratory quinones were MK-6 and MK-7. The major fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, iso-C15 : 1 G, summed feature 3 (C16 : 1?7c/C16 : 1?6c), iso-C15 : 0 3-OH and C16 : 0. The DNA G+C content of strain E403(T) was 37.9 mol%. Phylogenetic analyses based on 16S rRNA gene sequences of members of the family Flavobacteriaceae showed that strain E403(T) formed a distinct evolutionary lineage within the stable cluster containing type strains Zhouia amylolytica HN-171(T) (92.2 % similarity) and Joostella marina En5(T) (92.4 % similarity). In addition to the large 16S rRNA gene sequence differences, E403(T) can also be distinguished from the reference type strains J. marina En5(T) and Sinomicrobium oceani SCSIO 03483(T) by several phenotypic characteristics and chemotaxonomic properties. On the basis of phenotypic, chemotaxonomic and phylogenetic properties, strain E403(T) is suggested to represent a novel species of a new genus in the family Flavobacteriaceae, for which the name Pustulibacterium marinum gen. nov., sp. nov. is proposed. The type strain is E403(T) (= CCTCC AB2012862(T) = CGMCC 1.12333(T) = KCTC 32192(T)). PMID:23416571

Wang, Guanghua; Zhou, Danyan; Dai, Shikun; Tian, Xinpeng; Li, Jie; Chen, Wen; Xiang, Wenzhou; Li, Xiang

2013-02-15

407

Dasyatispora levantinae gen. et sp. nov., a new microsporidian parasite from the common stingray Dasyatis pastinaca in the eastern Mediterranean.  

PubMed

A new microsporidian infecting the Mediterranean common stingray Dasyatis pastinaca (Linnaeus, 1758) is described from Iskenderun Bay, Turkey. The parasite invades the disc muscles, producing slender, spindle-shaped subcutaneous swellings that develop into massive, elongated, tumor-like protuberances measuring up to 11 x 4 cm. Severity of the infection may vary from light (1 or 2 small lesions) to intense, with large parts of the dorsal surface covered with lumps and protrusions. These masses contained a yellowish-white caseous substance consisting of degraded host tissue and microsporidian sporophorous vesicles, which in turn contained developing sporonts, sporoblasts and spores. The ripe spore contained a uni-nucleate sporoplasm and large posterior vacuole, and measured 3.8-4.3 x 2.6-2.8 microm. Infection prevalence was 21% in a sample of 143 host individuals examined. All the infected stingray individuals were within the weight class of 300 to 800 g (200 to 305 mm disc width). Phylogenetic analyses of rDNA sequences indicate that this microsporidian belongs to the Pleistophoridae and clusters with species of the genera Ovipleistophora Pekkarinen, Lom & Nilsen, 2002 and Heterosporis Schubert, 1969. However, the morphology, development and host differ distinctly from all reported species, including those belonging to these 2 genera, and it is thus assigned to a newly erected genus and named Dasyatispora levantinae gen. et sp. nov. This is the first record of a microsporidian infection in a batoid. It is also the first microsporidian species to be formally described from an elasmobranch. PMID:21387993

Diamant, Ariel; Goren, Menachem; Yoke?, M Baki; Galil, Bella S; Klopman, Yaelle; Huchon, Dorothée; Szitenberg, Amir; Karh